Khan Noonien Singh ( alternate reality ) Khan Noonien Singh ( or simply , Khan ) , was the most prominent of the genetically - engineered Human Augment s 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 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 . After gaining his revenge on Admiral Marcus , he was later stopped by the crew of the and returned to cryogenic sleep . Biography . 20th - century origins . Records of the period , including Khan ' s origins , are vague . He was the product of a selective breeding or 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 internal massacres or wars of aggression . In the mid - 1990s , the Augment tyrants began warring among 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 , 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 , named for the site of the Australia n 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 ) three - hundred - year sublight journey . ( ; ) 23rd - century return . Following the destruction of Vulcan in 2258 , Admiral 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 . Soon after , he discovered the SS " Botany Bay " adrift . Despite knowing Khan ' s history , Marcus decided to bring him out of cryogenic suspension , believing his savagery and superior intellect would be prime assets to his cause . Having his voice and physical appearance heavily altered , Khan was reawakened and recruited under the identity of Section 31 agent , " John Harrison " . Marcus 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 . Disgruntled , Khan tried to smuggle his crew away in advanced long - range torpedo es 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 Khan replaced his Starfleet Academy ring with a bomb . After his daughter was cured with a vial of Khan ' s blood and its regenerative platelet s , 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 , Khan 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 Khan . Knowing that Marcus would call an emergency meeting in the light of the bombing , Khan rigged a combat efficient jumpship with a portable transwarp beaming device and headed to the Daystrom Conference Room . Once the conference was underway , Khan appeared and laid waste to the conference , killing , Captain Abbott and many other high ranking Starfleet officers . disabled the jumpship , but Khan beamed himself away before it crashed . He arrived in the one place Starfleet could not go : Qo ' noS , the Klingon home world . Undeterred , Kirk was granted permission by Marcus to travel to Qo ' noS and fire 72 experimental photon torpedoes on Khan ' s location . However , at the behest of his crew , Kirk chose to defy his orders and opted to arrest Khan instead . While Kirk led an away team with , , and , acting captain transmitted a message to Khan , warning him to surrender or be destroyed by the newly designed shipboard torpedoes . Suspecting the newly designed torpedoes were the very torpedoes he smuggled his crew into , Khan sought out the away team to confirm . Khan found Kirk , Spock , and Uhura being attacked by a Klingon patrol and single - handedly killed dozens of Klingon s . Confronting the landing party , Khan asked how many torpedoes the 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 . Khan then surrendered to the landing party . Kirk , angry that his mentor ' s murderer had saved them , punched Khan repeatedly but was unable to render him unconscious . From the brig , took a blood sample to analyze the secret behind Khan ' s superhuman strength and abilities and injected it into a dead tribble . Khan 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 to investigate , while McCoy and Marcus ' s daughter opened up a torpedo and discovered a cryogenically frozen man within and realized that he was 300 years old . Khan finally explained who he was to Kirk , and revealed that the torpedoes contained his fellow surviving Augments as part of a cover - up . Marcus appeared in the " Vengeance " and demanded Kirk hand over Khan . Kirk refused , and the " Enterprise " warped back to Earth with the intent of putting Khan on trial , which would certainly expose Marcus in the conspiracy . As Khan predicted , " 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 suit s 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 also 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 stunned Khan while Kirk admonished Marcus for compromising the Federation . However , Scott ' s phaser stun only temporarily subdued Khan , who quickly recovered and flung himself at Scott and Kirk , overpowered them , then stomping upon Carol ' s leg . Khan then used his bare hands to crush Marcus ' s skull , extracting revenge on his once tormentor . 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 once they were beamed over , crippling the " Vengeance " before she could destroy the " Enterprise " . 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 western North America , 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 could not guarantee that Khan would make it . The " Vengeance " slammed into the old prison on Alcatraz Island , careened across San Francisco Bay , and then plowed into several buildings , demolishing several skyscrapers . When the " Vengeance " crashed into the city , Khan leapt 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 medbay , McCoy had just examined Kirk ' s body when the dead tribble on his desk came back to life . The fight took the two combatants on to two automated barges . Spock had the advantage of creativity , and extensive knowledge of martial arts , but Khan had the superior advantages of superhuman strength , speed , thought and durability . Spock attempted to subdue Khan with a nerve pinch but Khan managed to overcome the pain . As Khan attempted to use his bare hands to crush Spock ' s skull , Spock managed to counter it with a mind meld . Near the end of the melee , with Spock again in Khan ' s cranial crushing lock , Uhura beamed down and fired several stun shots to distract Khan . Spock tore a piece of metal from the barge and broke Khan ' s arm before knocking him out . As Spock repeatedly pummeled an unconscious Khan , Uhura revealed that they needed Khan alive to save Kirk . After his blood was used to revive Kirk , Khan was placed back in suspended animation with his crew from the " Botany Bay " . ( ) Memorable quotes . " " I can save her . " " " " What did you say ? " " " " Your daughter , I can save her . " " " " Captain , are you going to punch me again , over and over , until your arm weakens ? Clearly you want to . " " " " 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 " . " " " " Why would a Starfleet Admiral ask a three - hundred year - old frozen man for help ? " " " " Because I am better . " " " " At what ? " " " " Everything . " " " " 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 ? " " " " 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 . " " " " 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 . " " " " My crew . . . is my family , Kirk . Is there anything you would not do . . . for your family ? " " " " If you think you ' re safe at warp , you ' re wrong . " " " " Captain , you can ' t even guarantee the safety of your own crew . " " " " You . . . You should have let me sleep ! " " " " 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 ? " " " " Well , Kirk . . . it seems apt to return you to your crew . After all . . . no ship should go down without her Captain ! " " " " NOOOOOOOOOOOOOO ! ! ! ! ! ! ! ! ! ! " " " " Set destination : Starfleet Headquarters ! " " Appendices . Background information . Bringing back Khan Noonien Singh was discussed before the release of ; on the film ' s audio commentary , it is stated the filmmakers considered having a shot of the after the credits , but opted out in case they decided not to use the character . Director J . J . Abrams said , " " 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 the character . Abrams commented that , in comparison to Nero from , the writers wanted " a much more nuanced and complex villain " for " Into Darkness " . ( " Cinefex " , No . 134 , p . 72 ) Due to the massive popularity of how Khan had been represented before , however , " there was a good year of debate , " explained Alex Kurtzman , over whether to include Khan in the upcoming movie . With a laugh , Orci phrased this issue , " " To Khan or not to Khan . " " Kurtzman observed , " " The choice to play in that sandbox is really complicated because when a character was as beloved as Khan , you really have to have a reason to do it . " " During the debate , Lindelof wanted to use Khan , while Orci was against this option . The filmmakers found a compromise by developing a story that would not entail Khan , and then determining if he could be " reverse engineered " into it . Stated Kurtzman , " " If we could take that [ tale ] and then incorporate Khan into the mix in a way that felt reverent and appropriate for that story , we would do it . Without that standard , we wouldn ' t [ … ] We all loved the ' Space Seed ' back story , the idea that he was a man who loved his crew as his family — that was the understandable and relatable agenda . And then we built outward from there . " " 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 story - line 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 , 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 code - name was April , another character Orci said he had considered as a villain . Once they chose to bring Khan into their film , the screenwriters were not necessarily eager to additionally incorporate a moment when the character ' s name is shouted in anger , as happens in , because they considered it vital that such a reaction be a natural and realistic one . Khan was portrayed by Benedict Cumberbatch . Before he was cast , Abrams approached Benicio del Toro for the role . Orci said they shied 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 , Orci stated , " " 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 . " " ( 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 blond 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 . The filmmakers considered giving Cumberbatch a shoulder - length wig , but Abrams felt he looked better without it . ( " Star Trek Into Darkness " iTunes enhanced commentary ) 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 that , 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 ! " " Recalling times when he had sneaked into screenings to see the audience ' s reaction to Khan revealing himself , Cumberbatch remarked that " to have that moment – that ' s worth any amount of subterfuge or holding back on reveals . " ( issue 289 , p . 23 ) The creative staff were ultimately very pleased with how Khan is depicted in " Into Darkness " . " " Ultimately , I think we felt that we found a reason and a way to do it that was all of the things we needed it to be , and yet really different , " " voiced Kurtzman . " I think the mistake that we could have made , that we didn ' t want to make , was to do a version of what Ricardo Montalban had done so brilliantly , and then fall short of that [ … ] There are things about Khan that are very familiar , and there are things that are entirely different , and that ' s exactly what we wanted to do . " " " However , Abrams voiced regret over keeping Khan ' s identity a secret . " " The truth is I think it probably would have been smarter just to say upfront ' This is who it is . ' It was only trying to preserve the fun of it , and it might have given more time to acclimate and accept that ' s what the thing was , " " he said . He added that hiding Khan ' s presence was mandated by the studio , who did not want to alienate non - " Star Trek " fans with the impression they had to learn about who Khan was to enjoy the film . Abrams agreed with that notion but " " wonder [ ed ] if it would have seemed a little bit less like an attempt at deception if we had just come out with it . " " Responding to Burk ' s comment that it might have hurt the film if the audience knew Harrison was Khan before Kirk did , Abrams added " " the truth is it probably wouldn ' t have made much of a difference in that regard . " " 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 . " " In the , the authors considered it possible that the red matter - created black hole caused differences in the past from the Prime Timeline . On page 414 of volume 1 , this is the information on the Khan of and : On the following page , this is the information on the Khan of Star Trek : Into Darkness : Apocrypha . 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 . According to his biography on the " Star Trek " movie app , " John Harrison " was born in 2228 in Dover , Great Britain , Earth to Richard and Sara Harrison . Harrison was one of nine survivors of the attack on the colony on Tarsus IV in 2246 , and both of his parents were killed in the attack . He graduated from the London School of Economics in 2250 . After graduating , he was appointed associate researcher , Starfleet Data Archive ( London ) , East Annex in 2255 . He was tasked with collection , organization and analysis of declassified data received from Starfleet - commissioned starships and from Federation member states . The virtual collectible card battle game " " uses two cards showing Khan : # 105 , titled Commander J . Harrison , and card # 111 , titled Human Augment Khan . The comic book series " " establishes Khan ' s history subsequent to the divergence of the timeline but prior to his encounter with the " Enterprise " . The Section 31 starship " Vanguard " discovers the " Botany Bay " and takes custody of Khan . Quickly using their databanks to determine his identity prior to awakening him , Admiral Marcus orders that Khan ' s face and voice 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 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 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 . Discovering that his crew is being held in the London facility and forging transmissions from Marcus , Khan is able to load his crew into the long - range torpedoes with the intent of stealing a starship with them aboard , but , before departing , Khan invades Marcus ' home and demands to know the truth before planning to kill him . The admiral , planning for Khan ' s rediscovery , has him targeted by a jumpship outside the window , forcing Khan to flee . His plan , now circumvented , forces him to coerce Thomas Harewood into destroying the London facility and set the events of the film into motion . " Star Trek : Khan " also establishes that he was originally an ordinary Indian boy named Noonien Singh and was an orphan living in an impoverished slum . In 1972 , he was captured , along with other impoverished children , and taken to a research facility to be a test subject for genetic engineering experiments . In August 1985 , as a young man , he escaped from the research facility , along with the other genetically engineered test subjects , and began a rebellion . He later gives himself the title of " Khan " , out of admiration for historical Mongol conqueror Genghis Khan , naming himself " Khan Noonien Singh " . Like the rest of the characters in the parallel universe of " Parallel Lives , Part 1 " and " 2 " , he has a . He also resurfaces in . Popular culture . 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 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 . " "