Khan Noonien Singh (Alternate Timeline)

"No ship should go down without her Captain!"

- Khan Noonien Singh after taking over the Vengance ship "You should have let me sleep!"

- Khan, before killing Alexander Marcus

"So, shall we begin?"

- Khan's most famous quote

Khan Noonien Singh, aka John Harrison, is the main antagonist of the 2013 film Star Trek Into Darkness. He is an extremely intelligent, ruthless terrorist, and a genetically engineered human being.

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

Background and Brainwashed by Marcus
"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, in the trailer

This version of Khan's backstory was the same as his prime reality counterpart's, until the destruction of Vulcan in 2258 changed the latter's future that led to the events of the movie from that point on.

Vulcan's destruction led Admiral Alexander Marcus of Section 31 to began a plan to militarize Starfleet, and he searched the galaxy for weapons to be used in a potential war with the Klingons. Discovering the SS Botany Bay, Marcus brought Khan out of stasis, believing his savage intellect would give him an advantage. Khan was then recruited into Starfleet under the new identity of Commander John Harrison, and tasked with designing weapons and ships for Starfleet, including the Dreadnought-class USS Vengeance.

The prequel comic Star Trek: Khan explains more reasons why Khan betrayed Marcus and how his ethnicity changed. When Khan was discovered, Marcus arranged for Khan's face and voice to be reconstructed from their Indian origins to a more Northern European origin. The admiral also had Khan's memory blocked with the intent of convincing him that he was 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, the Klingon homeworld.

Harrison 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 regains his memories.

Betrayal and Stealing Transwarp Beaming Equation
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, 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 Lieutenant Commander Montgomery Scott's transwarp beaming equation.

Attemp Murder at Daystorm Institute
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 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 attacked the conference, injuring many and killing Admiral Christopher 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. 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.

Revealing Marcus' True Nature
While Kirk led an away team with Spock, Lieutenant Nyota Uhura, and Hendorff, Lieutenant Hikaru Sulu, in temporary command of the USS Enterprise, 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 the patrol. Confronting the Starfleet officers, Harrison asked how many torpedoes the Enterprise had aboard. After Spock informed him of the count, which corresponded exactly to the number of his Botany Bay crewmembers 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 uncover the secret behind Harrison's superhuman strength and abilities. Harrison refused to answer Kirk's questions, instead giving him coordinates to a spacedock near Jupiter where the Vengeance was constructed, and suggested that Kirk open one of the torpedoes. Kirk contacted an absent Scott and gave him the coordinates to investigate, while Dr. McCoy and Dr. 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 and fired on it as it arrived in Earth's solar system. Marcus then beamed up Carol and prepared to destroy the Enterprise; fortunately for the Enterprise, Scott, who had sneaked aboard the Vengeance, deactivated its weapons.

Truce With Kirk and Betraying Enterprise Crew
Kirk and Khan then performed a space-jump to the Vengeance. Meanwhile, Spock consulted Spock Prime, his older counterpart from the prime reality, regarding whether he ever encountered Khan in the past; Spock Prime responded that he had, that Khan was dangerous, and that it had required a great sacrifice to stop him.

Aboard the Vengeance, Kirk, 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 attacked Scott and Kirk and broke Carol's leg before crushing her father's skull with his bare hands before her very eyes. 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 his deal with Spock. However, Spock, having predicted Khan's betrayal following his talk with Spock Prime, detonated the torpedoes, crippling the Vengeance. Khan cried out in anguish at the apparent loss of his crew (in actuality, Spock had earlier ordered McCoy to remove the stasis pods from the torpedoes much to Kirk's disgust due to Khan now angrier than ever).

The damage sustained caused both ships to be drawn in by Earth's gravitational pull. To prevent the Enterprise from crashing into San Francisco, Kirk sacrificed himself while re-activating the ship's warp core. Khan, on the other hand, directed the Vengeance on a crash course for Starfleet Headquarters, though the ship's computer informed him the ship would not hit its target. When the Vengeance crashed into San Francisco, Khan leaped down from the wreckage and posed as a shocked survivor.

Defeat
Moments later, Spock beamed down to execute Khan and avenge Kirk's death. An exciting chase ensues, with Spock pursuing the superhuman onto automated flying barges. A climactic fight erupts between the two, which Khan gradually wins. 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.

Reception
Khan's portrayal in Star Trek: Into Darkness by Cumberbatch receives criticism as much as it being acclaimed due to considering that the character had been "whitewashed into oblivion", from both critics and fans alike. Reason of this was due to in previous films, Khan was actually in Indian ancestry, not European. There have been similar accusations of whitewashing by fans and American Sikhs, with Star Trek: Voyager actor Garrett Wang tweeting "The casting of Cumberbatch was a mistake on the part of the producers. I am not being critical of the actor or his talent, just the casting". George Takei, the original Hikaru Sulu, was also disappointed with the casting, as he thought it would have been better to cast Cumberbatch not as an established villain like Khan but as a new character. On Trekmovie.com, co-producer and co-screenwriter Bob Orci addressed Khan's casting: "Basically, as we went through the casting process and we began honing in on the themes of the movie, it became uncomfortable for me to support demonizing anyone of color, particularly any one of Middle Eastern descent or anyone evoking that. One of the points of the movie is that we must be careful about the villain within US, not some other race".

Although, this was rectified with Star Trek: Khan which reveals that when Marcus brainwashed him, Marcus also had his face and appearance more European like through surgery. All of it was happened as result of the destruction of Vulcan's homeworld by Nero previously.

Trivia

 * This incarnation of Khan is the third main villain in a Star Trek film not to be killed, first being V'Ger and Whale Probe. Of these, he is the first who is not a probe.
 * He is the main villain of the second film in the reboot series. His Prime Reality Counterpart was the main villain of the second film in the original series as well.
 * He is similar to Raoul Batty from Blade Runner (Do Androids Dream Of Electric Sheep?)
 * Both are Genetically modified Humans and are ruthless
 * Both are villains set in the Future
 * Both have Genius Level Intellect
 * Both Brutally kill another villainous/Corrupt  character by crushing their skull or pushing their eyes to the back of their head.
 * Both wear long Trenchcoats