Dr. Nefarious

"What do you expect!? I'm a SUPERVILLAIN!!! Muhahahahahahaha! Bon voyage...losers!"

- Dr. Nefarious as he escapes alongside Lawrence from Magnus in Cronk and Zephyr's ship "No! Get away from me! And..do not stick that thing in... (yelps and screams in pain) Quit...trying to repair me, you moron! (groans and grumbles in pain as Repairbots leave, then grabs one and pulls himself out) I... AM... NOT-A-ROBOT! (looks down at hands and starts laughing) Hehehehehahaha... Hahahahahahaha...Bwahahahahahahahahaha!"

- Nefarious' Villainous Breakdown and evil laugh in the mid-credits scene of the 2016 movie.

Doctor Nefarious is a robotic mad scientist-turned dictator who hated organic life forms, despite formerly being one himself, and the main antagonist of the Ratchet & Clank series. He is the archenemy of the equally-infamous so-called superhero Captain Qwark, and later the most recurring foe and arch-nemesis of the courageous duo Ratchet and Clank.

Nefarious was the main antagonist in Ratchet & Clank: Up Your Arsenal and Ratchet & Clank Future: A Crack In Time, a hidden antagonist in Ratchet & Clank Future: Tools of Destruction and Ratchet & Clank Future: Quest For Booty, and then made a notable appearance in Ratchet & Clank: All 4 One as a playable anti-hero turned protagonist. He was also a cameo character and mentioned in games like Ratchet: Deadlocked and Ratchet & Clank: Into The Nexus. He was also responsible for the Amoeboid attack on Blackwater City in the first game, Ratchet & Clank.

Nefarious also appears as the main antagonist of the 2016 animated feature film and Playstation 4 game.

He was voiced by Armin Shimerman.

Personality
Dr. Nefarious is characterized as a deranged, eccentric, and egomaniacal scientist who sadistically shows no remorse for his actions and pleasure in villainy. He is also very conceited and egotistical, with his inventions often being made in his own image, and many of his robotic servants resembling him or sharing his mannerisms. He has an extreme hatred for organic life, referring to organic life forms as "squishies" and seeking to exterminate them or transform them into robots. Even when putting aside his hatred towards them in order to further his goals, he vowed to eventually destroy them again once he was finished.

Nefarious is also shown to be cunning and manipulative, able to manipulate many to work for him. He was able to fool the fongoids, the terachnoids, the Valkyries, and the Zoni to ally with him, before betraying them all. However, while working with them, he was often completely impatient, hot-tempered, and argumentative towards them when they fail him. While he is normally a traitorous betrayer towards his allies once he has obtained his goal, when it seems clear that they will useless and uncooperative with him, he will betray them prematurely.

Towards the end of All 4 One, Nefarious' companionship with Ratchet, Clank, and Qwark appears to have changed him, being close to tears when looking at a photograph of the four of them.

Appearance
Dr. Nefarious is a humanoid-structured robot-like creature during his robot form, he has a huge green head, probably a reference to him being smart, orange and purple body color, a large mouth, during his robot form, he has a green dome on his head, with gears inside, red glaring eyes, and mechanical wings.

His appearance does change at times though, in Up Your Arsenal, he has more highlights around his body, and some blue features. In A Crack in Time, he has pretty much the same colors, but has a different facial expression and a larger head dome.

In All 4 One however, his color scheme is entirely different, a purple body, shorter and slimmer body, a bigger head, and a exaggerated torso.

Pre-Ratchet & Clank
In high school, Dr. Nefarious attended the same 9th grade biology class with Copernicus Qwark where they were taught by Mr. Bozell. He had been constantly bullied and humiliated at the hands of Qwark, who was three times Nefarious' size and 26 years old at the time. His treatment included Qwark giving him wedgies, pouring lab beaker liquids on his head, cleaning chalk boards with his pants (while Nefarious was still wearing them), and being called "that freak with the headgear." Because of this treatment and his difficulty with Biology, Nefarious would slowly come to despise anything biological. Later, he attempted a career as a scientist, only to be shunned and called insane. (In the re-imagined series, this is changed, as he was originally the only member of the Galactic Rangers' support team before Elaris and Clank, but ridicule and mockery by Qwark, poor working conditions and budget cuts, being called "King of The Nerd Herd" and unacknowledged for his work drove him to pursue his career as a villain.) These experiences pushed Nefarious over the edge, and he set out to get revenge on all who had mocked him, especially Qwark.

Vid-Comic backstory
Dr. Nefarious eventually became a supervillainous mad scientist, while at the same time, Captain Qwark became a semi-fraudulent famous celebrity "superhero". The doctor started his campaign for revenge by creating the vicious Amoeboid creatures and launching an invasion on Blackwater City. After Captain Qwark defeated his "pets" and troopers, saving the burning city, Nefarious and his robotic servant, Lawrence, were forced to retreat in a rocket shuttle. Nefarious swore that he would have his vengeance "even if it takes a thousand years!" as his ship took off. Qwark managed to grab onto the rocket and held his breath tight. He clung to the ship for six days, and it arrived at the doctor's base on planet Magmos. Qwark used a disguise to sneak into the base, unaware that Nefarious was watching him. The doctor commented that Qwark's poor disguise made him appear more stupid than ever, and ignored a solemn insult from Lawrence: "Even drooling imbeciles can achieve success in certain fields, sir. Mad science, for example..."

Dr. Nefarious decided to wait as Captain Qwark fought through his defences. The two soon confronted each other face-to-face on a narrow catwalk overlooking churning gears and machinery. Qwark seemed to have met Nefarious before, but he claimed they hadn't, trying to hide the truth from his nemesis. Qwark soon recognized the doctor from "Mr. Bozell's 9th grade biology class," reminiscing on the "good times" of when he humiliated Nefarious, truly oblivious to just how much his treatment had affected the doctor. Qwark said he should give Nefarious a wedgie "for old time's sake." While trying to grab him, he accidentally knocked him off of the catwalk into the spinning gears below, prompting Nefarious to scream Qwark's name furiously as he fell. Turning away from his nemesis' grotesque fate, Qwark then casually walked away, confident that his rival was gone for good. As he made his escape, Qwark failed to notice a robotic hand pushing itself out of the rubble.

Dr. Nefarious had been forever changed into an advanced robotic being. This fit along well with his already immense contempt toward biological entities due to his miserable classes. Nefarious, much more powerful than before, resolved to continue his attempts to have revenge on the captain, and destroy all organic life in the galaxy, referring to organic life forms with the contemptuous name "squishies."

A short time later, after Captain Qwark returned to his condo in Metropolis, Dr. Nefarious attacked the city with a massive horde of robotic locusts that consumed various forms of matter. He commanded his servants to bring him Qwark's head; however, despite the damage they inflicted on the city, Qwark eliminated the threat they posed and once again confronted his nemesis. Qwark and Nefarious promptly battled in close-quarters one-on-one combat. Despite the vast array of superpowers he had been granted from his transformation, Nefarious was defeated once again, greatly damaged and left as a disembodied head (which is ironic, as he had hoped to have Qwark's head). Qwark threw Nefarious' head in a trash can as he screamed his revenge. The captain was then suddenly attacked and knocked out from behind by Lawrence, who had returned to aid his master after picking out torture chamber curtains. Nefarious urged Lawrence to hurry them away from Kerwan with Qwark in tow.

They then imprisoned him on Nefarious' Ice World. Captain Qwark, still asleep, had a brief dream, but soon woke up shocked. He asked where he was, locked in a cage descending from the ceiling by a chain. Dr. Nefarious, still a mere head held by Lawrence on a silver platter, explained "You're in my secret prison, awaiting the most ingenious and depraved punishment I can possibly imagine!" The doctor and butler then left for Nefarious' massage, which Lawrence was less than cheerful about. Qwark managed to escape the prison, accidentally setting off the alarm and causing acid to rise from the floor. Making it out, he retreated to his hideout on the Thrann Asteroid, where he hid until Nefarious allegedly disappeared. In reality, he was being repaired by Lawrence and was given a new body. However, Lawrence mistakenly attached Nefarious' head backwards. Nefarious could not see his arms, and looked down, asking frantically "Whose butt is this?" The doctor angrily screamed at his apologizing butler, causing himself to malfunction. The doctor was completely frozen as his brain began to pick up signals from a soap opera, Lance and Janice. Lawrence said that he would need to repair the glitch, then chuckled and said that it would be done "one of these days." However, the glitch never got fixed because the only highlight of Lawrence's days at work was getting to slap him so that he would unfreeze.

Ratchet & Clank
During the events of the first game, Nefarious did not appear. However, his Amoeboids attacked Blackwater City but the Amoeboids were driven back by Ratchet and the Rilgarians. Unfortunately, as it would happen many times over in the future, Captain Qwark successfully claimed full credit for this, when in reality, he simply executed "emergency response plan number two", in which he coordinated with the city's defenses from inside the women's restroom at the nearest local Galaxy Burger, something briefly noted in Episode Two of the Captain Qwark Vid-Comic Series, Arriba Amoeba!.

War on "the squishies" (Ratchet & Clank: Up Your Arsenal)
Ten years later, Dr. Nefarious started an entire public campaign to rid the Solana Galaxy of organic life forms. Nefarious formed an alliance with the Tyhrranoid race, who served the doctor as his personal army, gullible and oblivious to the fact that Dr. Nefarious transmitting to all the robots within the Solana Galaxy. they were organic life forms. The heroic duo, Ratchet and Clank, saw a news report detailing an attack on planet Veldin, Ratchet's foster home, by Tyhrranoid soldiers. Dr. Nefarious was believed to be the attack's mastermind. Later, on the Starship Phoenix, that fact was confirmed; Captain Sasha, Ratchet and Clank were listening to a distorted distress call from the Galactic President, who was requesting assistance to stop a Tyhrranoid invasion force on the Capital City of Marcadia. The message was then completely cut off by a galaxy-wide broadcast from Nefarious, who made his introduction to his new enemies from his office on Aquatos.

Warning to the "squishies" and Skirmish at Tyhrranosis
Dr. Nefarious the began broadcasting to the Solana Galaxy his message to all who opposed his dictatorship. In the message, the diabolical doctor dramatically announced his entire plot, while Lawrence acted out his words so that the deaf and hard-of-hearing could understand. Ratchet and Clank then managed to stop his attack on Marcadia. Later on, Clank explored Nefarious' Office in his "impenetrable" secret base on Aquatos, and found out that he was a huge fan of the Secret Agent Clank Holo-Vision series, having the entire episode collection, which disturbed Clank. Lawrence informed Nefarious of the break-in on his ship, the Leviathan, while he was watching Secret Agent Clank, which the doctor referred to as his "work." This news outraged the doctor, and caused him to crash and pick up soap opera signals again. After being smacked back to normal, he ordered Qwark's Q-Force, which Ratchet and Clank were a part of, annihilated for opposing him. The team's next mission was an attack on the Tyhrranoid homeworld, Tyhrranosis, where Ratchet and Clank defeated the Momma Tyhrranoid.

Biobliterator
As the Q-Force listened to Ratchet's recount of the fight on the Phoenix, Dr. Nefarious and Lawrence transmitted to them via hologram, mocking them. The doctor declared "I could obliterate the lot of you, and they wouldn't even mention it in Supervillain Weekly!" Nefarious was referring to a holo-vision show that he was often interviewed on about his evil schemes. He then said he had "far grander plans" for 'Agent' Clank. He then maniacally laughed, trying to end the transmission with a triumphant, intimidating appearance. The hologram remained on, followed only by awkward silence. Nefarious then had to whisper to his butler to turn off the transmission. Lawrence did so, having ruined his superior's moment with his spiteful sarcasm.

Daxx
Ratchet had Big Al trace the signal of the message back to the source. He showed them that it came from a facility on planet Daxx. He also patched through a video from Supervillain Weekly of Nefarious and Lawrence at the facility. The doctor and butler were being interviewed about Dr. Nefarious' new top secret superweapon constructed on Daxx. The interviewer said "Dr. Nefarious, we've all enjoyed your past work, but how do you respond to critics who say your latest galactic schemes are just more of the same?" Nefarious responded with a loud "I will annihilate them!" Lawrence could not comment with any details of the superweapon, but changed the subject and said "We do, however, have a lovely view of the ocean at sunset." Nefarious happily nodded in agreement at this, taking a bit away from his evil image. The announcer finished the broadcast with "Is Dr. Nefarious poised on the brink of galactic domination, or is this 'superweapon' just the latest in a series of maniacal pipe dreams? Stay tuned for more, from Supervillain Weekly!" Ratchet and Clank then explored Daxx, and found out the device was the Biobliterator. Nefarious had removed all data on the device, but it was deciphered that it had been transported to the Obani Moon System.

It was also revealed, through the Anti-Squishy Music Video that robotic pop star Courtney Gears was in league with Dr. Nefarious. He used her music as propaganda to spread his vendetta against organics, being a big fan of hers. Gears was apparently in love with Nefarious, giving him the pet name "Snooky Wookums," though this annoyed him greatly, and he valued her as an ally, but kept their relationship professional.

Holostar Studios
While at Holostar Studios, Clank needed to film a Secret Agent Clank scenario, with Gears as a character. After the shoot was over, he asked her what Nefarious was planning, and she was able to capture Clank by knocking him out. She then contacted Nefarious, who was greatly annoyed by her reference of "Snooky Wookums," and told her to bring him 'Agent' Clank. In a secret office supposedly at the studio, Nefarious had commandeered at the studio, he tried to turn Clank over to his side, as he was a fanatic of his series and believed it to be real, following his 'missions' from the beginning. The doctor even rejected Clank's assurance that the series was just an act, calling the statement "Lies! Squishy lies!" His anger caused him to freeze and pick up soap opera signals again. Gears had to smack him to get him back to normal. When Clank refused to join, Dr. Nefarious decided to replace Clank with a doppelgänger, Klunk. Posing as Clank, he told Ratchet that Nefarious was aboard the Leviathan.

Later on, Nefarious launched an attack on Blackwater City, which was also stopped by Ratchet. He and Klunk then went to Obani Draco, Gear's headquarters. Ratchet was shocked to witness a recording from the testing lab for the Biobliterator, which had since been transported away from the moon: Gears had used the machine to transform Skid McMarx into a robot. Ratchet thought this impossible, but Klunk said "Not for Dr. Nefarious..." The Lombax then defeated Courtney Gears in her studio, and received a transmission from Captain Sasha.

Dr. Nefarious and the Leviathan Trap
Dr. Nefarious' starship, the Leviathan, had been tracked to the Zeldrin Starport, where it was refueling. Ratchet, Klunk and Qwark then met up to infiltrate the ship. As soon as they arrived on board, Klunk secretly received a message from the doctor to lure them to the bridge. They soon located Nefarious, greeted casually by Lawrence. Commenting that Qwark had gained weight since their last encounter, Nefarious was angered by Qwark saying that "Courtney Gears didn't seem to mind." He went into yet another crash sequence, prompting Lawrence to happily smack him across the face. Nefarious declared he would have the last laugh, as he lured Qwark and Ratchet so that he could witness their demise. He then activated the self-destruct for the ship and commanded Lawrence to teleport them away. Lawrence left himself, leaving Nefarious behind. The doctor was not amused by this, and was teleported out moments later after shouting to him. While Ratchet and Klunk escaped, Qwark seemed to go down with the ship, trying to grab something.

Battle of Metropolis
After Captain Qwark's funeral, Ratchet deduced that Dr. Nefarious was planning on making good on his vow to destroy Metropolis, which was shown from years earlier in the Qwark Vid-Comic, Deja Q All Over Again. He traveled to Kerwan and took part in the large-scale battle, searching for Nefarious. Meanwhile, watching the battle from a Hover Train, Nefarious showed Clank Klunk's transmission of Ratchet's actions, meaning he could track the Lombax. Nefarious found the whole prospect delightfully amusing, laughing diabolically and trying to get his butler to go along with him. Lawrence merely said "You put the wit in 'twit', sir." Taking this as a compliment, Nefarious continued laughing happily. He declared that it would be the dawning of a new era, all thanks to his years of secret plotting and patience with many disappointments. The doctor arrogantly rebuffed Clank's confidence in Ratchet's abilities, claiming that Ratchet would be killed with Clank having a "front row seat." As Ratchet traversed through his forces, Dr. Nefarious revealed the Biobliterator itself.

He tried demonstrating its ability to transform any organics into robots, demanding the activation device from Lawrence. Proclaiming the new "Age of Robots," the doctor pressed the remote; however, it instead turned on a video recording of his first Galactic Idol audition. His butler had given him the wrong switch, angering him and causing him to furiously knock him over. 'Apologizing,' Lawrence gave his superior the correct remote and assured him he could continue. Looking away in case it was another error, Nefarious pressed the activation device, delighted to see it successfully activate the Biobliterator. As he laughed evilly, the machine rose up, transforming his remaining Tyhrannoid soldiers into Robonoids. Ratchet fought through these new metallic enemies and soon found out that the robot at his side was Klunk, Clank having been captured by Nefarious, who casually waved at Ratchet when he reached the Hover Train.

The doctor mocked Ratchet before leaving with Lawrence, laughing so hard that his sides began to ache from all his laughter throughout the day. However, he did admit that Ratchet was a far better adversary than the "imbecile" Qwark was. Ratchet fought Giant Klunk on the Hover Train and managed to defeat him and save Clank. Nefarious then launched a Robonoid attack on Aridia, which was again stopped by Ratchet and Clank. Meanwhile, Nefarious piloted the Biobliterator to different planets across Solana and turned many into robots, making it look like there was more than one due to the speed of the attacks. Ratchet and Clank went to the Crash Site of the Leviathan, thinking that whatever Captain Qwark had tried to grab as the ship exploded may have contained some sort of clue. They discovered that Qwark had gotten away from the ship's destruction in an escape pod and went into hiding for some reason. They also retrieved a data disc, which is what the captain had been trying to get. Back on the Phoenix, Ratchet gave Al the disc to decode, which would take him some time.

Battle Plan
It was decided that they would defeat Nefarious without the now-alive Captain Qwark, though their words about the situation caused Qwark to rethink his position. Ratchet then received a distorted message from Captain Sasha on the Phoenix, which was under brutal assault from Dr. Nefarious' troops. She told them that whatever was on the disc Captain Qwark had found had Nefarious worried, and he was prepared to destroy the team to get it back. Ratchet hurried to the ship and fought past the doctor's attack force. He reunited with his comrades on the bridge, and thanks to Al successfully decoding the disc, they found Nefarious' entire battle plan to attack planet after planet all over the galaxy, creating an entire population of robots in Solana. The doctor was confident that the Q-Force would never be able to stop the Biobliterator. Sasha told Ratchet that the machine was recharging at a base on Koros. Ratchet was determined more than ever to stop Nefarious after he learned that his next target was Veldin. After the duo fought their way into the base, Clank used the Nefarious BFG ion cannon to destroy the Biobliterator while Nefarious was screaming furiously from a video screen. Captain Sasha then contacted the duo, informing them that Al had finished decoding the disk.

Battle of Mylon (Final Battle)
It was discovered that Dr. Nefarious was preparing to use his second Biobliterator, more powerful than the first, and it was being fueled on Mylon, his master control center. Ratchet and Clank were able to defeat the last of Nefarious' Robonoids and approached him at the Biobliterator's fueling dock. As they got to him, Nefarious and Lawrence teleported into the Biobliterator, which flew away, done fueling at the last moment. Nefarious laughed maniacally as his machine flew away, confident his plans would succeed. They pursued him to the Launch Site, where the doctor had already initiated the launch sequence. Ratchet confronted Nefarious as he operated the take-off procedure from a console that had a green color scheme and dome reminiscent of the doctor's own. Nefarious was rather annoyed to see Ratchet interfering with his plans once more, expressing how the "miserable rodent" would pay for his "insolence."

As the doctor furiously monologued, Ratchet threw his wrench at him. Dr. Nefarious barely managed to dodge the wrench as it crashed into and destroyed the console. Ratchet declared that Nefarious' flight was canceled, and the enraged doctor called Lawrence to his side. Nefarious waited impatiently, continuing to shout his butler's name, as he would not appear. A hologram of Lawrence then answered, to which Nefarious ordered Ratchet's annihilation. The hologram revealed itself to truly be Lawrence's voicemail, asking for a name and brief message before vanishing. Nefarious then said, frustrated, "Fine. I'll do it myself."

Dr. Nefarious faced off against Ratchet and Clank in close-quarters combat, proving to be a formidable adversary thanks to his powers. He soon decided to fool Ratchet into believing he had won the fight in order to give himself time to escape. He knelt down on the ground, faking coughs and whimpering, and declared that he had no choice but to throw himself on Ratchet's mercy. The Lombax, initially shocked, then triumphantly stated that the doctor's reign of terror had ended and fell for the ruse. Ratchet did not expect Dr. Nefarious to rise from the ground, activate a forcefield around himself, and fly away. Nefarious shouted "Sucker!" to his foe as he escaped, laughing mockingly. Angered by this, Ratchet pursued Nefarious to the battlefield where his remaining troops and the floating Biobliterator waited. With help from the Galactic Rangers, the duo broke the doctor's final defenses and confronted Nefarious beneath the Biobliterator. Despite exhausting almost all of his abilities, Nefarious was bested in combat and knocked to the ground.

Dr. Nefarious again called Lawrence to his aid, who actually appeared this time, dressed in a rockstar costume. The butler was reluctant to follow Nefarious' orders, having been preoccupied with guitar practice, which he clearly saw as more important. Picking himself up and dusting off, the doctor ordered his butler to "Begin the transformation!" and shouted at him when he continued to be distracted by his guitar. At Lawrence's pressing of the activation device, the second Biobliterator changed into an immense mechanoid. Nefarious broke into a diabolical laugh as he and Lawrence teleported to the cockpit, ready to depart and bring about the mad scientist's Age of Robots; however, as he began firing at Ratchet and Clank on the ground, he was shot at by Captain Qwark, who arrived on the scene in his own shuttle. He had decided to come out of hiding to help defeat his nemesis, wanting to be a true hero. Distraught at this, Nefarious yelled in frustration "No! I don't believe it!", and Qwark replied with "Believe it, toasterhead!"

The Asteroid
Ratchet, Clank and Qwark managed to defeat Dr. Nefarious in the air and destroyed the second Biobliterator. The head of the mechanoid landed on the battlefield, and Nefarious was greatly humiliated by being defeated at the hands of "squishies," believing he would never live it down. The cockpit's computer announced that the reactor would detonate in sixty seconds. Nefarious then bluntly told Lawrence to engage the teleporter. Lawrence asked him to specify a destination, and Nefarious said "Who cares? Just get us out of here." The computer then said time was up, and he shouted "What!? That wasn't even close to sixty seconds!" The computer childishly responded with "Buh-bye!", prompting a terrified expression on the two. Right before the Biobliterator's head exploded, Lawrence teleported them away in a panic, having no time to pick a destination for them.

Dr. Nefarious and Lawrence were stuck far away on an asteroid in space, unable to teleport to another planet, as they were well out of range. According to Lawrence, it would be five or ten thousand years before something came for them to teleport to. Nefarious shouted angrily in disbelief, and then sat on the ground. He then said "Now what?" as his butler looked at him. Lawrence asked him "I don't suppose you can play drums?", wanting someone to go along with his guitar to pass the time. Infuriated by this ridiculous question, Nefarious screamed at his butler.

Ratchet: Deadlocked
While Lawrence spent most of their drifting playing his guitar, Nefarious simply sat thinking over and over about his failure, which would continue to haunt him. While stranded Lawrence told Nefarious that they were coming within range of a space station. Unfortunately, it exploded mere minutes before they passed it. Furious at Lawrence, Nefarious shouted his butlers name at the top of his lungs, only for another transmission of Lance and Janice to play in his head.

Secret Agent Clank
During Secret Agent Clank, Klunk made a copy of Nefarious which had his abilities and was programmed to obey Klunk. He was destroyed by Clank in the final confrontation with Klunk.

Zanifar
The two were still forced to aimlessly drift through space. After some time, the asteroid drifted to the Polaris Galaxy. In Polaris, the two seemed to briefly come upon planet Mukow, as the doctor's wallet was found and held at a concession stand.The pair also spent much time drifting through the Breegus System, even being spotted by space pirates in the Corvus Nebula while Dr. Nefarious was having one of his malfunctions and screaming at Lawrence, playing an episode of Lance and Janice. Despite Lawrence's claim of the time it would take for them to find refuge, the rock picked up speed and turned into a ball of fire after drifting to planet Zanifar. It crashed in the Tobalia village of a local Fongoid tribe, forming a crater, which was barricaded. Nefarious and Lawrence sought refuge with the tribe, arriving as they were in the middle of celebrating spring break.

While living with the Fongoids on Zanifar, Dr. Nefarious tried to decipher how he could have lost everything he had worked so hard to accomplish to his enemies. He even spent one night twitching and cradling himself in a darkened room after drawing several pictures of Ratchet and Clank on the wall, crayons clenched in his hand and mouth. Nefarious decided to go on a spiritual journey to find the answers he sought. He spent his time on Zanifar studying Fongoid meditation, attending numerous anger management classes, and dabbling in yoga. Eventually, he went on a spirit walk on planet Quantos. It was here that he learned of the mystical Zoni race, who were in charge of protecting the universe and keeping it in balance. He also discovered their ultimate creation: the Great Clock, a facility in the center of the universe (give or take fifty feet) which kept the flow of time and effectively acted as the cosmos' greatest contingency plan.

The Zoni
Nefarious secretly plotted to gain control of the clock to rewrite history, making it so no villain would ever go through such a humiliating defeat as he did, and so that heroes would always fail in their righteous endeavors up to the present. With this plot, he temporarily put aside his organic life form vendetta, again working with "squishies" if it suited his plans. Dr. Nefarious fooled the Fongoids into believing that he was loving, kind being, and they came to worship him. Cancelling their spring break, he used them as a task force to help construct the Tombli Outpost in their Tobolia valley, which he used as his temporary base of operations. It would go on to be the primary manufacturing plant for his new army of starships and Nefarious troopers. He then made new allies with other villains who also wanted to use the clock for their own ends. He hired former Terraklon mercenary and assassin, Lord Flint Vorselon, to serve as the field enforcer of his troops. Vorselon had lost his body in a battle against the Drophyds on Zaurik, being confined to a cyborg suit. In addition to bolt payment, he was promised to have his original body and glory restored with the clock's power. The doctor also got into contact with Pollyx Industries and formed an alliance with the Terachnoid CEO, Pollyx, who signed his corporation and most Terachnoids in an exclusive contract to work for the doctor, now having access to valuable Zoni technology and knowledge. With assistance from the labor and resources of the Fongoids, Pollyx Industries worked toward building the Nefarious Space Station, which would be the doctor's headquarters.

As his station was under construction, Dr. Nefarious kept his evil activities in the Tombli Outpost secret from the Fongoids and waited to reveal his devious schemes to the rest of the Breegus System. Using Pollyx's holdings, he managed to contact the Zoni leader, Orvus, requesting an audience with the fellow scientist. A being of etiquette, Orvus honored the seemingly friendly robot's wishes and traveled to the outpost. He was then taken by surprise and imprisoned.

As Lawrence stood by with Pollyx and a Protomantis, Dr. Nefarious interrogated Orvus about getting inside the Orvus Chamber, the Great Clock's control room that commanded the flow of time. He tortured Orvus when he repeatedly refused, having his machine, the Hypersonic Brainwave Scrambler, blast him with sonic energies, a vulnerability of the Zoni. Nefarious failed to heed Orvus' insistence that time was not to be tampered with as he continued to grow weary of the torture. Nefarious shouted at Pollyx when the interrogation continued to fail, as Pollyx was scanning Orvus' brain for the key to the chamber but could not find it. Pollyx believed that the Zoni had erased his own memory, and Nefarious gave him one final chance to tell him how to access the chamber. Orvus again refused, and Nefarious furiously clenched his fists over his head before again signaling his device to blast him. Orvus held off the blast, saying that the only one who would enter his chamber was safe, far from the doctor.

The growing light of the held-out beam made Dr. Nefarious and all present cover their eyes. Orvus then dissipated in a flash, and Nefarious frantically asked where he went. Unable to deduce where Orvus had gone, Pollyx still managed to pull up an image from his memory scanned before he vanished. The image was the schematics of Nefarious' old nemesis, Clank. It was revealed that he was in fact Orvus' heir and the key to entering the Orvus Chamber. The doctor planned to get a hold of Clank through the Zoni, who were still unaware that the doctor had kidnapped their leader. Nefarious contacted the Zoni and offered to help them find Orvus' heir so that they could bring him to fulfill his destiny. When Ratchet and Clank came to Polaris and defeated Emperor Tachyon and his empire, Nefarious led the Zoni to their new master. They aided Clank in the journey to vanquish the Cragmites, appearing before him on occasion.

Ratchet & Clank Future: Quest for Booty
Nefarious and the Zoni eventually brought Clank to the Great Clock to understand his purpose. Ratchet soon set out to find his dear friend, unaware of Dr. Nefarious' new schemes. After battling space pirates and learning a bit about the Zoni through the travel journals of Captain Darkwater, Ratchet retrieved a Fulcrum Star and used it to power an Obsidian Eye on planet Merdegraw. With it, he traced the Zoni and Clank's location to the Breegus System and managed to catch a brief glimpse of the Great Clock during a visit from Nefarious; Clank's logic and memory seemed to be dysfunctional, and the Zoni relied upon the doctor to repair him. He then appeared, slightly silhouetted in the doorway of the mnemonic station where Clank was being held. Ratchet watched as he walked down the stairs, being revealed in the light bit by bit, but then slipped on a feather duster left carelessly on the floor by his butler, which caused him to fall down the stairs screaming. Fully revealed, Nefarious was shown angrily shouting at Lawrence once again.

Ratchet and Talwyn Apogee were then given coordinates to the Breegus Nebula, the entrance to the system where Dr. Nefarious had resurfaced, as the signal was lost. Ratchet vowed to rescue his friend and defeat Nefarious once more as he and Talwyn departed from Hoolefar Island. While Ratchet took off in the Aphelion beside Captain Qwark, who was eager to get back into 'the hero business' after doing some film acting, Talwyn stayed behind, warning Ratchet that where he was headed was home to a great deal of mercenaries. It was these very guns-for-hire that would assist in Nefarious' new plot and prove to be a large obstacle for Ratchet.

Ratchet & Clank Future: A Crack In Time
When the Nefarious Space Station was eventually completed, Dr. Nefarious revealed his true villainous colors and imprisoned the Fongoids in work camps around the Tombli Outpost. The base was fitted with much security after the doctor went to his new station, a statue also being made of him before the entrance to the outpost in a triumphant stance in front of the asteroid he had drifted on for so long. It was at this point that the doctor's evil campaign was made fully public. He took control of the Bernilius Sector where his station was located, and further imposed his will on the Phylax Sector, Vela Sector and Corvus Sector thanks to the influence of Lord Vorselon and Pollyx Industries, sending fleets and satellites out to keep the system under secure watch. With Nefarious' army on the rise, an exiled Lombax freedom fighter, General Alister Azimuth, began battling his forces to try and save Polaris. Through his fight with the elder general, Nefarious discovered the full history of the Lombaxes and Ratchet.

For over a year, as his henchmen enforced his will throughout the Breegus System, Dr. Nefarious and Lawrence continued to visit the Great Clock and keep a false alliance with the Zoni, using the pretense that he was repairing Clank as a facade to keep their trust. He was often opposed by the facility's Junior Caretaker, Sigmund, who tried to save Clank, knowing full well that all Nefarious wanted was the Orvus Chamber. Each time the doctor tried unlocking Clank's memory banks, the neural safeguard would lock him out. His constant failures, along with his overall annoyance of pretending to be friends with the Zoni, frustrated Nefarious greatly. During a visit, he mocked the unconscious Clank floating in the mnemonic station, saying "Ah, my arch nemesis... Not so smart now, are you?!" and banging his head. Lawrence then informed his superior that the Zoni had been inquiring about their progress once more, angering the doctor.

The Zoni then entered the room, reminding Nefarious that he must fix Clank. He assured them that he was doing his job and again entered the brain's system, trying to arrange Clank's memories correctly to see into his subconscious. He was once again locked out, nearly having a breakdown in his frustration. Nefarious then exclaimed "It's in here, Lawrence! Somewhere in this brain lies the key to the Orvus Chamber!" Upon hearing this, the Zoni firmly told Nefarious he was forbidden from accessing the chamber, as it was only meant for the Senior Caretaker of the Great Clock, which was Clank. His insistence going to no avail, Nefarious betrayed them and activated the Hypersonic Brainwave Scrambler. It's sonic wave attacks forced the Zoni out of the room. As Nefarious laughed maniacally, the room went completely dark; a black-out had occurred in the clock, as the equipment was also especially susceptible to sonic weaponry like the Zoni themselves, something which Lawrence apologized for not mentioning earlier.

The back-up generators restored power seconds later. When the lights came back on, Dr. Nefarious saw that Clank had managed to awaken from his slumber and escape in the darkness. Nefarious angrily ordered Lawrence to stop him as he fled. Over the loudspeakers and appearing on large projection screens beside Lawrence, Nefarious asked Clank to come back so they could discuss things "robot to robot." The doctor's troops, meanwhile, were firing at the fleeing Zoni and Clank, causing much damage to the clock in the process. Lawrence informed Nefarious, who frantically told his troops he wanted to Clank alive. The robot soldiers did not obey Nefarious' commands, as damage had been done to their hive mind in the ensuing chaos, and Lawrence needed to reboot them. They also detected that Sigmund was trying to aid Clank's escape. Nefarious ordered Lawrence to reset the locks and track the "meddlesome" caretaker's location.

All the while, Dr. Nefarious' troops were chasing after the Zoni, who continued to flee and evacuated the clock. Upon hearing the dropping number of Zoni from Lawrence, Nefarious told them to come back, exclaiming that he was just kidding, and joking about how they had kidnapped Clank thanks to him. When Clank knocked over a neatly stacked pile of crates belonging to the doctor at Sigmund's behest to get ahead in his escape, Nefarious threatened Sigmund, saying "When I get my hands on you, I'll rip that dome of yours off, and pull out your brain with my bare hands!" Lawrence sarcastically complimented the doctor's "tough talk," truly not finding it intimidating at all. While Clank escaped his troops, Nefarious told Clank he would not be able to fly to Polaris and that if he wanted to keep his brain, he should surrender. Sigmund's location was eventually discovered to be in a broom closet, and Nefarious had him locked off from Clank for the time being. Clank then stopped at a balcony, with no other escape. Nefarious and Lawrence confronted him on the platform, where Nefarious dared him to jump, and then laughed mockingly. Clank then asked where his old enemy had taken him. Nefarious showed Clank his home, the Great Clock, and described its location and history.

Clank wondered what lie Dr. Nefarious had told the Zoni and believed that the doctor had sought vengeance. Nefarious found it odd how Clank thought he went to all the trouble he did of taking over the clock for mere vengeance, and said "They say I'm ego-maniacal". He then said that "it's...all in the past." He had Lawrence use the orb of gratuitous immobilization to freeze Clank and knock him out. Lawrence suggested they use the Mnemonic Station again, but Nefarious said he had better plans. When Lawrence questioned this, he said "Patience, Lawrence. We have all the time in the universe..." Nefarious then returned to his space station and began rehearsing an original play he wrote: Night of the Living Squishies. He used his robot troops as actors to practice scenes, and gave out several script books. He had his soldiers line up at the door outside his personal chamber, where he was rehearsing scene four of act three. In the scene, Nefarious held Captain Qwark at gunpoint while the captain tried to capture him. However, Nefarious' rehearsal was repeatedly halted when he accidentally killed the troops playing Qwark with the pistol he was using, which was supposed to be unloaded.

The more troops went in to attempt the part, the more of them were killed, and the more the line outside shook with fear. Meanwhile, back in the Great Clock, Sigmund was teaching Clank things about traversing through the security systems and dealing with enemies. They encountered the Hypersonic Brainwave Scrambler, which had been left loose in the clock, crashing into and damaging much machinery even after the Zoni it was chasing had escaped. Upon destroying the sonic device, Clank and Sigmund continued onward through the clock, but were silently being watched by Lawrence, who had remained in the clock to keep an eye on them on Nefarious' orders. He contacted Nefarious via hologram, inadvertently interrupting yet another one of Nefarious' rehearsals, upsetting the doctor.

Lawrence reported to him that Clank was en route to the Orvus Chamber. Dr. Nefarious laughed with delight at this news, as he wanted Clank to lead him directly to the chamber. Nefarious prepared to go back to his play, but Lawrence informed him of another matter, showing him a video camera on Vorselon's warship of Ratchet and Qwark rescuing the locked up Fongoids they had come to the Breegus System and were fighting the doctor's forces to try and rescue Clank. This revelation greatly angered Nefarious, and again triggered his malfunction, causing him to pick up more radio signals of Lance and Janice. Lawrence had the robot troop in the room whack Nefarious over the head, and he went back to normal. Nefarious ordered Lawrence to kill them so they could not meddle in his plans. Proclaiming he would carry out his orders, Lawrence suggested Nefarious engage the safety on his gun so as not to kill any more troops.

Nefarious shouted at Lawrence that the blaster was not even loaded, and tried to demonstrate this by aiming it off to the side and pulling the trigger. A shot did fire, bouncing off the walls of the room until it hit the frightened robot trooper. Frustrated by killing another one, Nefarious went over to his desk and hit the red button to buzz the door open, shouting "Next!" to signal another trooper in. As the door opened, all of the shaking troops hesitated to enter, fearing they would end up like those auditioning before them. Through the rest of the Breegus System, Ratchet and Qwark continued their attempts to find Clank, and were eventually assisted by Azimuth, who wanted to rectify his mistakes and bring back the Lombaxes with Ratchet via the Great Clock. In Axiom City, Ratchet discovered a large amount of Nefarious' hold on Polaris, and confronted Pollyx himself. Tossing aside the weak alien, Ratchet and Azimuth discovered the location of another Obsidian Eye, which they planned to use to get in touch with Clank. After, they received a transmission from Dr. Nefarious. He was glad to see Ratchet would witness his greatest triumph, and that he had met the "shame" of the entire Lombax race.

Ratchet asked if Nefarious was still up to his old plans, such as "Trying to turn everyone into robots", or "good old-fashioned galactic domination" and the doctor pondered whether he should allow Ratchet to find out or just kill him. As Nefarious ended the transmission, an alarm went off in the Pollyx Industries building, alerting that a large destructive machine was tearing through the city: the VX-99. Nefarious had sent it in to annihilate Ratchet and Azimuth, and it was destroying the area to ensure they did not escape. Ratchet managed to defeat the monstrous machine, and continued to come after Clank. Back at the Nefarious Space Station, Lawrence again contacted the doctor via hologram. They were discussing the procedure to rewind time with clock. In order to reset everything according to Nefarious' needs, Lawrence said Pollyx had estimated that the procedure would take 183 temporal paradoxes, and 184 should the Blarg participate. Since Dr. Nefarious wanted to make it so every hero would lose their battles in the past, it seemed he would enter into an alliance with the Blarg, among Ratchet and Clank's other defeated enemies.

Lawrence advised that Pollyx's scientists examine the Orvus Chamber before testing the clock. Nefarious then leaped in front of Lawrence's holographic image and said "What's the matter, Lawrence? Chicken?" He then imitated a chicken to mock his butler, and at that moment, Lord Vorselon teleported into the room and loudly announced the doctor's name. The sudden announcement behind him caused Nefarious to let out a startled scream and jump high into the air. As he fell back down, Lawrence pretended to try and catch him, only for him to fall right through the hologram and hit the floor. Lawrence then sarcastically apologized as his superior picked himself up, and Nefarious simply scowled at him. Going back to his desk, Nefarious listened as Vorselon gave his report. He had discovered that the two Lombaxes had destroyed the VX-99, and he was tracking them. Nefarious angrily proclaimed "Unacceptable! I practically handed those squishies to you on a silver platter. How could you be so utterly incompetent?!".

Dr. Nefarious threw a small glass globe sitting on his desk at Vorselon in anger, but Vorselon avoided it by teleporting out of its way, leaving it to shatter against the wall, and then reappearing behind Lawrence's hologram, shivering with fear at Nefarious' rage. As Lawrence left them alone, the doctor reminded Vorselon that if the Lombaxes found the clock, their plans would be ruined, and his body would never be recovered. Nefarious declared he would bring in "specialists", and pressed the button to buzz his office's door open. Three large female robots walked in: Cassiopeia, Carina and Libra, leaders of the Valkyrie mercenaries. Nefarious had requested an audience with them at his station. The doctor introduced them individually, referring to Libra with distaste compared to Carina and Cassy due to her masculine voice and behaviour. Nefarious reminded them of how their original colony had been lost decades ago in the tragic Erebus supernova. He requested their services in exchange for returning their lost colony.

The Valkyries accepted, and along with Vorselon, fought against Ratchet and his allies while Nefarious got closer to accomplishing his goal. Eventually, Ratchet managed to contact Clank, and Clank told him to confront Nefarious in the past on Zanifar so that he could save Orvus. Using a time portal projected by Sigmund, Ratchet went through a series of events both in the present and past Zanifar, and eventually got inside the Tombli Outpost in the past, right when Nefarious was interrogating and torturing Orvus. After Orvus vanished and Clank's image appeared, Ratchet exclaimed in confusion, alerting Nefarious to Ratchet's presence. However, Ratchet had taken out a Constructo Bomb Glove grenade, and threw it at Nefarious before fleeing. The bomb exploded inches away from the doctor's face, and as he yelled in agony, it was shown in slow motion that he was knocked back. His right eye was damaged, a crack forming up the side of his green dome, his red pupil knocking loose, and giving Nefarious a permanent scar on his face.

The Doctor angrily ordered his troops to annihilate Ratchet, but the Lombax escaped back to the present. Back at the Nefarious Space Station, in the present, he was sitting on his coach with Cassiopeia, laughing while he told her of how he mocked Clank as a prisoner. Cassy grew closer to the Doctor, saying "Dr. Nefarious, you have such a wonderful sense of humor, and you're so, so..." However, Nefarious suddenly realized what Ratchet had done. The bomb scarring his eye in the past took effect in the present, and Nefarious said "Uh oh..." as the scar formed and his eye fell limp. He then angrily screamed Ratchet's name. Much later, Ratchet fought Vorselon in combat, for the second time, and Vorselon revealed his new suit had been upgraded by Nefarious. He was still defeated, once again escaping, head intact, returning to the Doctor's station. In Nefarious' office, the two played against each other in a holo-vid game with Dr. Nefarious fighting Captain Qwark.

Lord Vorselon's Qwark character was at a disadvantage because Vorselon had no arms. Defeating him, Nefarious loudly gloated in Vorselon's face and sat back down. Lawrence then appeared in a hologram and reported that he had captured Clank and the Orvus Chamber, as Clank had unknowingly led them right into it just as Nefarious predicted. Pleased with this news, Nefarious told Lawrence to notify the Valkyries, and mobilized the next phase of his plans: Unnecessarily Evil Initiative Omega-91. Lawrence went to inform the Valkyries of the next step in their plot, and Nefarious' door bell rang the next moment. A light voice said that it was time for Nefarious' massage, but the annoyed Doctor pointed out he did not send for a massage. He told the person at the door to go away, but the voice briefly got deeper and again asked him to open the door. When it opened, a female nurse appeared, and Nefarious' loose eye fell limp again. It was Qwark in another poor disguise, and the Doctor recognized him, but played along with his ruse, making the Captain believe he was fooled.

When the Lombax hero and elder antihero arrived, Nefarious was complaining with Cassiopeia about trying to kill Ratchet as per Unnecessarily Evil Initiative Omega-91's procedure. Ratchet later successfully defeated and killed Cassiopeia on Vapedia and rescued Clank, the Valkyries finally beaten completely, although Lawrence did not know what happened on Vapedia. The reunited duo left the Valkyrie Citadel and headed toward the Nefarious Space Station, where the disguised Qwark aided them in getting inside their enemy's stronghold. Alister wanted to misuse the Great Clock to change history and bring back the Lombaxes, leaving the team when Ratchet and Clank refused to let this happen. Clank managed to sneak in an air duct and came to a vent above Nefarious' office. There, Nefarious told his computer to take his dictation: "Things to do once the clock is under my control. Number 1: Double-cross remaining Valkyries and retire Lord Vorselon. Number 2: Reestablish vendetta against organic life forms! And number 3: Iron socks." This revealed that Nefarious intended not to keep the deals he made as his subordinates had failed him for too long. Clank successfully scanned the Doctor after he was done recording his to-do list. This allowed Ratchet to apply a holo-guise of the doctor and freely explore the station undetected. Despite this, Ratchet's height did not change, but Nefarious' minions still fell for the trick.

Getting updates in Dr. Nefarious' plot from Lawrence, the disguised Ratchet wanted him to order Nefarious' fleet to land at the station. This could not be done until Ratchet destroyed the nearby asteroids blocking the landing bay with the station's Hypernova Defense Laser with help from Pollyx who he sent to the brig. Ratchet made sure all the vessels that he could contact landed. After all the ships landed, Ratchet used the laser to destroy every ship as well, giving Nefarious no escape from his station. As Ratchet and Qwark made their escape, they were confronted at the bottom of an elevator by the real Nefarious, flanked by two guards. Qwark, still believing his facade was working, quickly said "You're not Dr. Nefarious!" to Ratchet and slapped him, accidentally deactivating his holo-guise. Ratchet told Nefarious that he could not use the clock, as nothing he could want was worth risking the entire universe. Nefarious said that there was, and he had his three greatest enemies to thank for it. He then had several flashbacks that showed everything he had been through since his first defeat at the hands of Ratchet and Clank, after which the Doctor explained his ultimate goal to the trio.

After capturing them following a futile escape attempt by Qwark, he attached Ratchet and Clank to an asteroid, prepared to launch from his Asteroid Flinger 5000, which he installed in case he ever needed a "super ironic death scenario." Ratchet said that the Doctor was making a mistake, and Nefarious said "Time will tell." Bidding farewell to his old nemeses, Nefarious laughed evilly as he prepared to press the launch button on the machine. However, while laughing, the Doctor again froze and picked up Lance and Janice signals. After an awkward pause, a nervous trooper standing by Nefarious took his hand and pressed the button. Ratchet and Clank were flung far away to Morklon, but eventually returned to the station. Lawrence had come from the clock in another ship, and the Doctor was preparing to return to the facility to finally complete his plans. He was distraught by the duo's return, thinking they were supposed to be dead, unaware that the Zoni had helped them in the crash.

Ratchet and Clank told Dr. Nefarious to shut down his transport and surrender on behalf of galactic authorities. He approached the duo and mocked Clank for "running right back to playing backpack to a squishy" rather than fulfilling his destiny. He told Clank "You're nothing but a pathetic sidekick," prompting Lawrence to sarcastically say "We should hang out some time" to Clank. Ratchet, angered by his mocking of Clank, stood up to the mad doctor, they then prepared to defeat Nefarious once and for all, and the Doctor rose into the air with booster jets in his feet and extending his stabilizer wings, saying that he would rewind time after killing the two so he could do it over and over again. Before attacking Ratchet & Clank, Nefarious ordered Lawrence to fall back to the outer perimeter, allowing no damage to befall their ship. A fierce battle immediately ensued, going around the ring of the platform near the station, which was eventually destroyed by the Hypernova Defense Laser after the Doctor ordered Lawrence to activate it. The battle then went onto Nefarious' ship as it flew away from the station, setting course for the clock.

Damage to the ship during the fight caused it to speed into an inevitable collision with the Nefarious Space Station, and Lawrence had no control over the auto-pilot. Despite getting assistance from his butler, Nefarious was defeated a second time, and fell screaming to his ship's surface. He then got up and began malfunctioning more than ever before due to the damage he sustained. He fell on his back with his mouth wide open as his brain picked up signals of opera music. He then sprang up as a lottery sound played, and fell forward. As the ship came closer to crashing into the station, Ratchet grabbed Nefarious and urged him to tell how to disengage the auto-pilot. The doctor would not respond, and his eyes continued to spin in circles while eccentric laughter was heard in his brain's signal. Ratchet smacked Nefarious to try and snap him out of it, but this merely caused the doctor to get up and dance to a yodeling tune in his brain. Nefarious then collapsed completely, his eyes popping out and the signals in his brain dying away. Lawrence then took the escape pod, leaving Ratchet, Clank and the crumpled body of Dr. Nefarious on the ship. However, Azimuth appeared and saved Ratchet and Clank before it collided as they jumped off the saucer and into his ship. Unbeknownst to anyone at the moment, Lawrence teleported the Doctor's unconscious body away. After the ship crashed into the dome of the station, it's head was given a scar and broken eye just like the original Nefarious. It then completely exploded, and the Doctor's villainous plot was finally ended.

During the credits, radio announcers Kip Darling and Pepper Fairbanks reported that the remains of neither Nefarious nor Lawrence were found anywhere in the station's rubble and that Polaris Defense Initiative 1887-Upsilon was mobilized to locate them; galactic authorities proceeded with a manhunt to find the missing Doctor and his partner, making the arrest of them their highest priority.

Ratchet & Clank: All 4 One
Nefarious appears again as the main antagonist at the very beginning and one of the four protagonists. At this point, the evil doctor and his butler's threat level had increased to from "unknown" to "alive and at large". With all the commotion, Galactic President Qwark acted on the situation, convinced that there was no danger, and assured the galaxy that everything was under control. Being interviewed by news reporters Kip Darling and Pepper Fairbanks via satellite, Ratchet and Clank gave their personal outlook on the predicament. They claimed they were retired and had full confidence that Qwark would be able to track down the enemy.

Meanwhile, in the depths of Planet Igliak, the doctor's new plan was already in motion. Dr. Nefarious set up a false award ceremony for the Galactic President, claiming Qwark was the world's greatest Intergalactic "tool" and that he would receive an Intergalactic Tool of Justice Award for defeating a Light-Eating Z'Grute in the past, which never occurred. Ratchet and Clank, suspicious of the award, went along with Qwark in receiving it. Out from behind, Dr. Nefarious and Lawrence on a miniature hovercraft appeared and the menacing doctor revealed his plan to the heroes, that which he would unleash the Light-Eating Z'Grute upon the city to kill them. However, in an unexpected turn of events, the Z'Grute raged uncontrollably, giving Nefarious no control over the creature. Reaching for Lawrence for help, Lawrence cowardly walked away, stating it was time for him to tender his resignation, leaving Nefarious forced to join forces with Ratchet, Clank and Galactic President Qwark to prevent the Z'Grute from causing more damage through the city of Luminopolis. The rare creature attracted the attention of a vast and powerful machine known as Ephemeris the Creature Collector. The heroes were accidentally transported to a marooned planet called Magnus by the machine, a planet containing a dark secret that not even its caretakers fully understand, and are forced to work together for their own survival in finding a way off the unknown planet. The foursome awake in a testing hub in an unknown location and are forced to participate in testing to disguise themselves as minions. The four soon encounter a little girl named Susie, who assists them in escaping the facility.

After escaping the creature collecting facility, the foursome encounter Cronk and Zephyr who report via hologram to inform them that they were traveling to Magnus to retrieve them but got stuck in an asteroid field and until they are assisted, there was no way for them to get them. Realizing they were trapped for good, the four gazed, stunned by the environment they were transported to. Susie then proceeded to direct the foursome to a small village inhabited by a race of creatures known as Tharpods, the natives of the planet. One of them informed the four of the background behind Ephemeris, claiming it to have been around for over a hundred years, snatching the universes' most dangerous creatures and transporting them to their planet. The native referred them to the Creature Collector's emissary, Commander Spog, who had been attacking the Tharpods and protecting the machine for years. The Tharpod figured Ratchet and Clank for candidates to help protect the planet from the chaos caused by Ephemeris and Spog, but Ratchet, retired from heroics, was unenthusiastic about going on another adventure to help, but confirmed he would notify the Polaris Defense Force to assist them once he was off the planet. Ratchet had a change of heart, however, when he heard Susie's parents were killed during Ephemeris' raid on Totem Fi, she was an orphan, and agreed to help track down Commander Spog. After destroying a wigwump while using jetpacks on their trail to Spog, Clank came across a holo-journal narrated by Frumpus Croid explaining the attack of Uzo City orchestrated by Spog and his armies and that the controller of Ephemeris had a plan for the creatures the machine had been capturing all those years. After a fight, Nefarious jokingly and insultingly commented that he wasn't going to carry the exhausted Qwark if he passed out and the pair continued their search for Spog.

The pair eventually tracked down Spog and after a long chase, defeated him. Spog was near-destruction, but agreed that if Nefarious repaired the damage they had caused him, he would, in return, tell them how to defeat Ephemeris. Once Spog was repaired, the commander told them that "only the architect who [lived] in the forest of the blue rocks" had the answers they were looking for. Qwark commended Nefarious' good actions, saying that "[he] did the right thing", to which Nefarious countered angrily, telling Qwark to "Get bent".

During the adventure, Nefarious constantly complained about Qwark and even tried to kill him at one point, though because Qwark moved Nefarious accidentally fell off the edge of a platform and was saved by Qwark, this filled Nefarious with uprise and gave him a change of heart.

Towards the end of the adventure, Nefarious started treating the others as if they were friends, and during the final battle against the Loki Master, Nefarious saved Qwark and dealt the finishing blow to the Loki, ultimately saving the universe.

After Cronk and Zephyr landed, Nefarious seemingly reasserted his supervillain attitude and escaped with Lawrence in their ship, but during the end credits Nefarious was seen looking at a picture of him with Ratchet, Clank and Qwark with a sad look on his face, as he was purely upset to have to leave his friends.

Ratchet & Clank: Full Frontal Assault
Nefarious did not appear in the story, instead he appeared as one of the multiplayer characters, he was available as part of the Villains Pack, alongside Tachyon and Drek.

The Ratchet & Clank Collection
Nefarious met Clank on a planet and they began insulting each other after watching the events of Up Your Arsenal. Nefarious claimed that he should have killed Ratchet and Clank when he still had the chance.

Crossover Appearance
PlayStation All-Stars Battle Royale Nefarious appears in San Francisco where his Nefarious Space Station is located, after some time he will move the players onto the station and begin attacking them with help from the Hypersonic Brainwave Scrambler. In this game he is allied with the Chimera, a species from Insomniac Games' Resistance series. Nefarious also appears as a Minion that is unlocked by reaching Level 80 with 3 characters.

Nefarious (along with the Helghan army from KILLZONE and Zeus from God of War) was originally going to be the final boss of PlayStation All-Stars Battle Royale, but was scrapped for Polygon Man.

Movie appearance (2016 reboot)
Doctor Nefarious, also called Neffie (by Drek), was a mad scientist and former Galactic Ranger, who manipulated the Blarg Chairman in order to gain vengeance. He is the main antagonist of the 2016 animated film Ratchet & Clank and its tie-in PS4 video game reboot. At the end of the movie he survives the destruction of the Deplanetizer, albeit seriously injured. Small robots called Repairbots who passed by transformed him into a robot, despite his protests. Nefarious lifted himself up and realized his new body actually was that of a robot, although he did not want it, and broke into a devilishly hysterical, then maniacal evil laugh.

Trivia

 * According to early concept art in Ratchet and Clank: Up Your Arsenal, Nefarious was originally going to be wearing a cape, instead of this, the final design resulted in him having the two metallic winglike tendrils protruding from his back.
 * Although he was implied to have been an organic before, this was only confirmed in the 2016 animated film and tie-in video game, ultimately until his transformation near the movie's end.
 * However, the new robotic form he emerges in is virtually identical to his basic designs from the original series.
 * Ironically, it presumably also deepened his conflict with and hatred for his Lombax archenemy by making Ratchet the one indirectly responsible for his physiological conversion.
 * Apparently, before Ratchet & Clank came along, Captain Qwark was the only person to ever defeat Dr. Nefarious in the original series.
 * Nefarious is effectively the main villain for the entire series; he has appeared more than the other villains, and has been fought by Ratchet & Clank more times.