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"Is there anything you would not do for your family?"
- - Khan Noonien Singh, 2259
Khan Noonien Singh (or simply, Khan), was the most prominent of the genetically-engineered Human Augments of the late-20th century Eugenics Wars period on Earth. Considered genocidal tyrants who conquered and killed in the name of order, Khan and his kind were frozen in cryogenic sleep.
In the 23rd century, Khan was revived by Admiral Alexander Marcus to design weapons and ships to prepare for war against the Klingon Empire. He was given a new identity, that of John Harrison, an English Starfleet commander. Khan, however, rebelled, and after believing his crew had been killed, he began a one-man campaign against Starfleet.
The enhanced platelets in his blood could heal severe injuries and illnesses which would otherwise be fatal.
Records of the period, including Khan's origins, are vague. He was the product of a selective breeding and genetic engineering program, based on the eugenic philosophy that held improving the capabilities of a man improved the entire Human race. Augments produced by the program possessed physical strength and analytical capabilities considerably superior to ordinary Humans, and were created from a variety of Earth's ethnic groups. Khan's background was suspected to be Sikh, from the northern region of India.
Khan lived up to the axiom coined by one of his creators, "superior ability breeds superior ambition". By 1993, a wave of the genetic "supermen," including Khan, had simultaneously assumed control of more than forty of Earth's nations. From 1992 to 1996, Khan was absolute ruler of more than one-quarter of Earth's population, including regions of Asia and the Middle East. Considered "the best of tyrants", he severely curtailed the freedoms of his subjects, but his reign was an exception to similar circumstances in Earth history – lacking massacres or internal war.
In the mid-1990s, the Augment tyrants began warring amongst themselves. Other nations joined in, to force them from power, in a series of struggles that became known as the Eugenics Wars. Eventually, most of the tyrants were defeated and their territory recaptured, but up to ninety "supermen" were never accounted for.
Khan escaped the wars and their consequences along with eighty-four followers (including Joachim, Joaquin, Kati, Ling, McPherson, Otto and Rodriguez), who swore to live and die at his command. He saw his best option in a risky, self-imposed exile. In 1996, he took control of a DY-100 class interplanetary sleeper ship he christened SS Botany Bay, named for the site of the Australian penal colony. Set on a course outbound from the solar system but with no apparent destination in mind, Khan and his people remained in suspended animation for Botany Bay's (nearly) two-hundred-year sublight journey. (TOS: "Space Seed")
Following the destruction of Vulcan in 2258, Admiral Alexander Marcus of Section 31 initiated a program to militarize Starfleet and began searching the galaxy for weapons to be used in the war with the Klingon Empire that he now believed was inevitable. Discovering the SS Botany Bay, Marcus brought Khan out of suspension, believing his savage intellect would be a prime asset. He forced Khan into working with him 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 under the new identity of John Harrison.
Disgruntled, Harrison tried to smuggle his crew away in advanced long-range torpedoes 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 his 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 the bomb and destroying the facility. In the midst of the chaos, Harrison used the opportunity to inspect a salvaged terminal to gain the confiscated formula for transwarp beaming.
Before he set off the explosion, Harewood sent Marcus a message, explaining he had been threatened by Harrison. Knowing that Marcus would call an emergency meeting in the light of the bombing, Harrison rigged a combat efficient jumpship with a portable transwarp beaming device and headed to the meeting location. Once the conference was underway, Harrison appeared and laid waste to the conference, killing Admiral Pike, Captain Abbott and many other high ranking Starfleet officers. James T. Kirk disabled the jumpship, but Harrison beamed himself away before it crashed. He arrived in the one place Starfleet could not go: Qo'noS, the Klingon homeworld.
Undeterred, Kirk was granted permission by Admiral Marcus to travel to Qo'noS and fire 72 experimental photon torpedoes on Harrison's location. However, at the behest of his crew, Kirk chose to defy his orders and opted to arrest Harrison instead. While Kirk led an away team with Spock, Uhura, and Hendorff, acting captain Sulu transmitted a message to Harrison, warning him to surrender or be destroyed by the shipboard torpedoes. Harrison found Kirk, Spock, and Uhura being attacked by a Klingon patrol and single-handedly killed dozens of Klingons. Confronting the landing party, Harrison asked how many torpedoes the Enterprise had on board. Spock informed him of the count, which corresponded exactly to the number of his former crew members which were still in stasis. Harrison then 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.
From the brig, 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; he instead gave him coordinates to the spacedock near Jupiter where the Vengeance was constructed, and suggested he open one of the experimental torpedoes. Kirk gave the coordinates for the absent Montgomery Scott to investigate, while McCoy and Marcus's daughter Carol opened up a torpedo and discovered a cryogenically frozen man within. Khan finally explained who he was to Kirk, and revealed that the torpedoes contained his fellow surviving Augments as part of a cover-up. Admiral Marcus appeared in the Vengeance and demanded Kirk hand over Khan. Kirk refused, and the Enterprise warped back to Earth so Khan could be brought to trial. The Vengeance caught up in subspace and fired on the Enterprise as it arrived outside Earth.
Marcus beamed his daughter over to the Vengeance and prepared to destroy the Enterprise but Scott, who had snuck aboard the Vengeance at its spacedock, deactivated its weapons. Kirk and Khan donned thruster suits to fly over and commandeer the Vengeance. Meanwhile, Spock consulted his older counterpart from another timeline regarding whether he ever encountered Khan Noonien Singh: the old Spock responded he had, that he was dangerous, and that it had required a great sacrifice to stop him. Kirk had grown suspicious of Khan and advised Scott to stun him once they had taken over the bridge of the Vengeance.
When they arrived on the bridge, Scott shot Khan while Kirk admonished Marcus for compromising the Federation. This did not subdue Khan, who flung himself at Scott and Kirk and broke Carol's leg before crushing her father's skull with his bare hands. Khan then sat in the command chair and ordered Spock to hand over the torpedoes or he would kill Kirk and resume bombarding the Enterprise. Spock obliged, and Khan beamed Kirk, Scott and Carol back into the Enterprise's brig, but reneged on the deal. Spock, having predicted Khan's betrayal, 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 ship crashing into San Francisco, Kirk sacrificed himself reactivating the ship's warp core. Khan, on the other hand, directed the Vengeance on a crash course for Starfleet Headquarters, though the computer predicted they would not make it. 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. In the Enterprise's sickbay, McCoy had just examined Kirk's body when the dead tribble on his desk came back to life.
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. Spock finally knocked Khan out. After his blood was used to revive Kirk, Khan was placed back in suspended animation with his crew from the Botany Bay. (Star Trek Into Darkness)
"Captain, are you going to punch me again, over and over, until your arm weakens? Clearly you want to."
- - Khan Noonien Singh to James T. Kirk
"John Harrison was a fiction created the moment I was awoken by your Admiral Marcus to help him advance his cause. A smoke screen to conceal my true identity. My name is... Khan."
- - Khan revealing his identity to Kirk and Spock
"Why would a Starfleet Admiral ask a three-hundred year-old frozen man for help?"
"Because I am better."
- - Khan and Kirk
"Alexander Marcus needed to respond to an uncivilized threat in a civilized time, and for that, he needed a warrior's mind - my mind - to design weapons and warships."'
"You are suggesting the Admiral violated every regulation he vowed to uphold, simply because he wanted to exploit your intellect."
"He wanted to exploit my savagery! Intellect alone is useless in a fight, Mr. Spock. You, you can't even break a rule; how can you be expected to break bone?"
- - Khan and Spock
"Marcus used me to design weapons to help him realize his vision of a militarized Starfleet. He sent you to use those weapons; to fire my torpedoes on an unsuspecting planet, and then he purposely crippled your ship in enemy space, leading to one inevitable outcome: the Klingons would come searching for whomever was responsible, and you would have no chance of escape. Marcus would finally have the war he talked about, the war he always wanted."
- - Khan, revealing Marcus' plans and intentions to Kirk and Spock
"I watched you open fire in a room full of unarmed Starfleet officers. You killed them in cold blood."
"Marcus took my crew from me..."
"You are a murderer!"
"He used my friends to control me. I tried to smuggle them to safety by concealing them in the very weapons I had designed. But I was discovered. I had no choice but to escape alone. And when I did, I had every reason to suspect that Marcus had killed every single one of the people I hold most dear! So I responded in kind."
- - Kirk and Khan
"My crew... is my family, Kirk. Is there anything you would not do... for your family?"
- - Khan to Kirk, trying to justify his actions
"If you think you're safe at warp, you're wrong."
- - Khan to Carol Marcus, shortly before the Vengeance fires on the Enterprise in subspace
"You should have let me sleep!"
- - Khan to Alexander Marcus before crushing his skull
"Well, let's play this out logically then, Mr. Spock. First, I will kill your captain to demonstrate my resolve, then if yours holds I will have no choice but to kill you and your entire crew."
"If you destroy our ship, you will also destroy your own people."
"Your crew requires oxygen to survive, mine does not. I will target your life support systems located behind the aft nacelle. And after every single person aboard your ship suffocates I will walk over your cold corpses to recover my people. Now, shall we begin?"
- - Khan and Spock, the former threatening the Enterprise
"Well, Kirk... it seems apt to return you to your crew. After all, no ship should go down without her Captain!"
- - Khan to Kirk on beaming him back to the Enterprise
- - Khan, witnessing the detonation of the torpedoes he believes contain his crew
"Set destination: Starfleet Headquarters!"
- - Khan, directing the crippled Vengeance to crash into San Francisco
Khan Noonien Singh (alternate reality) appears in:
Bringing back Khan Noonien Singh was discussed before the release of Star Trek: on the film's audio commentary, it was stated the filmmakers considered having a shot of the SS Botany Bay after the credits, but opted out in case they decided not to use the character. J. J. Abrams felt "It'll be fun to hear what Alex and Bob are thinking about Khan. The fun of this timeline is arguing that different stories, with the same characters, could be equally if not more compelling than what's been told before. [...] Certain people are destined to cross paths and come together, and Khan is out there... even if he doesn't have the same issues." 
Co-writer Damon Lindelof said the jumping off point for the sequel's story was deciding whether Khan would be the villain, and he, Kurtzman and Orci weighed the pros and cons of using him.  Lindelof wanted to use him, while Orci was against it. They compromised by developing a story would not entail Khan, and then determining if he could be "reverse engineered" into it.  Eventually, Orci felt "the details became too juicy to avoid. Genetic super man from a time that understood war and savagery, etc. Once we had a basic structure that did not necessarily necessitate him, we were able to tailor the script itself to details and inspirations that he brought."  Lindelof added the storyline avoided "The audience [knowing] something the bridge crew did not, which was 'Whatever you do, don’t wake that dude up.' So we didn't want to put the bridge crew behind the audience in terms of what they knew about Trek." 
Khan's undercover name was inspired by his name in an early draft of the script for "Space Seed", John Ericssen. Orci said "We shot the movie using the name Ericsenn [sic] but decided it would give it away[,] so we cheated the name Harrison into everyone's mouth!"  According to John Eaves, the character's production codename was April, another character Orci said he had considered as a villain.  
Khan was portrayed by Benedict Cumberbatch. Before he was cast, Abrams approached Benicio del Toro for the role.  Orci said they shyed away from casting an Asian actor as Khan because "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." He also stated the "true essence" of Khan's character was "that he was a genetically engineered superman," "not where he was from or the color of his skin."  In response to a question asking whether Khan's appearance was "cosmetically altered to avoid detection", Orci said that the theory was an "Interesting idea. Could be." . Also, in answer to a question about Khan's change in features, he said "uhm…. one of his abilities is that he is a shape shifter?" 
Cumberbatch commented the role was "daunting because of the legacy involved and the amount of speculation about [Khan] possibly being the villain." (Empire issue 289, p. 23) Lindelof said of writing for Cumberbatch that "when you can get [a] monologue to come out of [his] mouth, does the 'writing' even matter? I mean, seriously, I made that guy say 'Milk, milk lemonade, and this is where the fudge is made' and it scared the living shit out of me." 
Cumberbatch was cast two weeks before filming. Mary L. Mastro, head of the film's hair department, wanted Khan to have black hair to contrast with the blonde Kirk. She recalled, "JJ called a meeting with the creators involved in what he was going to look like and [Cumberbatch] walks into the room with super-short blond hair. My mouth dropped open, like, 'Oh, great.'" The schedule was altered slightly to give more time to determine Cumberbatch's appearance in the film. Costume designer Michael Kaplan wanted Khan to be "dapper", giving him "a number of very long, elegant coats. It's nice, even in the distance, to be able to recognise a character right away. He's pretty high fashion-looking." 
Cumberbatch trained one-to-one with his stunt double Martin De Boer, learning basic martial arts. De Boer described Cumberbatch as "'very receptive to learning. I've had actors who want to be an action star but don't want to put in the work, and he was the opposite, he said, 'I want to train as much as I can.' He was very committed. Besides working with us, he was working with his personal trainer five, six days a week; he really got in shape." De Boer said because of Khan's strength, Cumberbatch "wanted to have more static and powerful movements. That strength changes the rules of the martial arts we use. You don't have to do five punches, you just have to use a couple of moves and he takes out the guy already." 
Bad Robot Productions went to great lengths to hide Khan's identity, even screening the space jump scene to the press with life sign readouts displayed as "Harrison" and Spock's lines referring to Khan overdubbed to refer to Harrison. Bryan Burk defended the strategy, stating "Even if you don't even know who Khan is, you know that you're watching a film where for forty-five minutes or an hour of the movie you are ahead of the characters. So you're just kind of waiting for them to catch up with what you already know, that he is not who he says he is."  Cumberbatch said the secrecy was fine for him, though Alice Eve did tease him, saying "The lies, Benedict, the lies!" He recalled that when he sneaked into screenings to see the audience's reaction to Khan revealing himself, that "To have that moment - that's worth any amount of subterfuge or holding back on reveals." (Empire issue 289, p. 23)
When asked if Cumberbatch could reprise the role, Lindelof replied "To answer that question would be to determine whether or not he actually survives this movie, but if he survives this movie, we would be incredibly stupid to not use him again."  As to whether Khan's blood could disrupt dramatic tension in the next film, Orci said they "figured there are so many horrible ways to die in space that no medicine could save you from that we would be okay." 
Cumberbatch also portrayed Khan / Harrison in three "Disruptions" videos to promote the film, in which he analyzes Kirk, Spock, and Uhura's weaknesses and declares he will threaten them. 
Entertainment Weekly saw parallels between the new Khan and figures such as Osama Bin Laden or Saddam Hussein, as both men were allied with the US before turning on them.  Simon Pegg commented "Iraq had nothing proven to do with 9/11, and yet Bush used that as an excuse to start a war with those people. You can always see the Klingons as like Iraq and John Harrison the proxy for Osama bin Laden." 
Lindelof further acknowledged the terrorism parallels in an interview with StarTrek.com, as Khan's 72 torpedoes reminded them of the notion of 72 virgins in paradise. Lindelof responded "Of course it is a coincidence, because that is a number taken from canon. It was pointed out to us at the scripting phase – the 72 virgins – and that actually gave us pause, because we didn't want people drawing that comparison... but there it is."