Khan Noonien Singh (Alternate Timeline)

"You think your world is safe? It is an illusion, a comforting lie told to protect you. Enjoy these final moments of peace, for I have returned to have my vengeance. So, shall we begin?"

- Khan Noonien Singh

Khan Noonien Singh, aka John Harrison, is the primary antagonist of the 2013 film Star Trek Into Darkness.

He was played by Benedict Cumberbatch, who also portrayed Smaug in the Hobbit film trilogy.

Biography
This version of Khan's backstory was remain same with his prime reality counterpart's, until the destruction of Vulcan in 2258 changed the latter's future that led to the events in the movie from that point on. Vulcan's destruction on that year droves Admiral Alexander Marcus of Section 31 to began a program to militarize Starfleet and searched the galaxy for weapons to be used in a war with the Klingons that he now believed was unavoidable. Discovering the SS Botany Bay, Marcus brought Khan out of cryogenic stasis, believing his savage intellect would be a key asset. He blackmailed Khan into his service by threatening to kill his fellow Augments, and set him to work designing weapons and ships for Starfleet, including the Dreadnought-class USS Vengeance. Khan was recruited into Starfleet under the new identity of Commander John Harrison.

In Star Trek: Khan comic books that serves as prequel for Star Trek : Into Darkness, explained more reasons why Khan later betrayed Marcus and how his recent visage and voice became more European than his prime reality counterpart's. When he was discovered, Marcus has arranged the orders for both surgery and brainwash on him before being awakened from cryo-sleep. The said orders was Khan's face and voice had to be reconstructed from their Indian origins to a more northern European origin and has his memory blocked with the intent of convincing Khan that he is John Harrison, a Starfleet researcher in London's Kelvin Memorial Archive, who lost his memories in an accident during a failed mission to Qo'nos.

He is later given the task of helping advise Section 31 on possible enhancements to Starfleet weapon, shield and propulsion technology (which is to be incorporated aboard the USS Vengeance) as well as taking on a mission to destroy Praxis with the help of a portable transporter he designed and built. The mission is a success (explaining the destroyed moon seen in orbit of the Klingon homeworld in the film), but, in the process, Khan rediscovers his memories of his true identity.

Disgruntled by everything that has happened to him, Harrison tried to smuggle his crew away in experimental photon torpedoes he himself had designed, but was discovered and forced to flee alone. Believing Marcus had killed his crew, he coerced Section 31 agent Thomas Harewood into betraying Starfleet by offering a blood transfusion for Harewood's terminally-ill daughter. Harewood agreed, and Harrison replaced Harewood's Starfleet ring with a bomb. After his daughter was cured with a vial of Harrison's blood, Harewood went to work at his office in the Kelvin Memorial Archive in London, where he dropped the false Starfleet ring into a glass of water, igniting a bomb and destroying the facility. In the midst of the chaos, Harrison used the opportunity to inspect a salvaged terminal to gain Montgomery Scott's formula for transwarp beaming.

Before he set off the explosion at the archive, Harewood sent Marcus a message, explaining he had been threatened by Harrison. Marcus called a summit at the Daystrom Institute, ordering a manhunt for Harrison. During the meeting, James T. Kirk, Christopher Pike's first officer, deduced that Harrison had not left Earth because he was aware that protocol would dictate that a meeting like this one would be held at that location. Harrison suddenly appeared in a jumpship and laid waste to the conference, injuring many and killing Pike. Kirk disabled the jumpship, but Harrison beamed himself away before it crashed. Later, Scott contacted Kirk and Commander Spock to inform them that Harrison had beamed himself to the one place Starfleet couldn't follow: Qo'noS, the Klingon homewold. Undeterred, Kirk was granted permission by Marcus to travel to Qo'noS and fire seventy-two experimental photon torpedoes on Harrison's location. However, at the behest of Spock, Kirk decided to arrest Harrison and bring him back to Earth to stand trial for his crimes.

While Kirk led an away team with Spock, Lieutenant Nyota Uhura, and Hendorff, acting captain Hikaru Sulu transmitted a message to Harrison on Qo'noS, warning him to surrender or be destroyed by the torpedoes. Moments later, Harrison found Kirk, Spock and Uhura being attacked by a Klingon patrol and single-handedly killed dozens of Klingons. Confronting the officers, Harrison asked how many torpedoes the USS Enterprise had on board. After Spock informed him of the count, which corresponded exactly to the number of his former crewmembers which were still in stasis, Harrison surrendered to the landing party. Kirk, angry that his mentor's murderer had saved them, punched Harrison repeatedly but was unable to render him unconscious.

Once aboard the Enterprise, Harrison was placed in the ship's brig. Dr. Leonard McCoy took a blood sample to analyze the secret behind Harrison's superhuman strength and abilities, and injected it into a dead tribble. Harrison refused to answer Kirk's questions, instead giving him coordinates to the spacedock near Jupiter where the Vengeance was constructed, and suggested that Kirk open one of the torpedoes. Kirk gave the coordinates for the absent Scott to investigate, while McCoy and Carol Marcus opened up a torpedo and discovered a cryogenically frozen man within.

When Kirk and Spock confronted him with what they discovered, Khan finally explained who he was to Kirk, revealing that the torpedoes contained his fellow surviving Augments as part of a cover-up. Not long afterward, Marcus arrived aboard the Vengeance and demanded that Kirk hand over Khan. Kirk refused and ordered the Enterprise to warp back to Earth so Khan could be brought to trial. The Vengeance caught up with the Enterprise in subspace and fired on it as it arrived outside Earth. Marcus then beamed up Carol and prepared to destroy the Enterprise; fortunately for the Enterprise, Scott, who had sneaked aboard the Vengeance at its spacedock, deactivated its weapons. Kirk and Khan then donned thruster suits to fly over and commandeer the Vengeance. Meanwhile, Spock consulted Spock Prime, his older counterpart from the prime reality, regarding whether he ever encountered Khan Noonien Singh; Spock Prime responded that he had, that Khan was dangerous and that it had required a great sacrifice to stop him. Meanwhile, aboard the Vengeance, Kirk, having grown suspicious of Khan, told Scott to stun him once they had taken over the Vengeance's bridge.

When the three of them arrived on the bridge, Scott shot Khan while Kirk admonished Marcus for compromising the Federation. However, Khan was not easily subdued and he flung himself at Scott and Kirk, and broke Carol's leg before crushing her father's skull with his bare hands. Khan then contacted the Enterprise and ordered Spock to hand over the torpedoes or he would resume bombarding the Enterprise. Spock agreed, and Khan beamed Kirk, Scott and Carol back aboard the Enterprise, but reneged on the deal. However, Spock, having predicted Khan's betrayal following his talk with Spock Prime, had ordered McCoy to remove the stasis pods and detonated the torpedoes, crippling the Vengeance. Khan cried out in anguish at the apparent loss of his crew.

The damage sustained caused both ships to be drawn by Earth's gravitational pull. To prevent the Enterprise crashing into San Francisco, Kirk sacrificed himself in the process of reactivating the ship's warp core. Khan, on the other hand, directed the Vengeance on a crash course for Starfleet Headquarters, though the computer informed him the ship would not hit its target. When the Vengeance crashed into the city, Khan leaped off the bridge and posed as a shocked survivor. Spock beamed down to execute Khan and avenge Kirk's death, pursuing him onto automated flying barges. Spock attempted to subdue Khan with a nerve pinch and then a mind meld, but to no avail. Uhura beamed down, firing several stun shots to weaken Khan and revealed to Spock that they needed Khan alive to save Kirk (McCoy had just discovered that Khan's blood possessed regenerative properties). Spock finally knocked Khan out. After his blood was used to revive Kirk, Khan was placed back in suspended animation with his crew.