In 1974 A.D. Kahn Noonien Singh, a genetically engineered human known as an "Augment", was born to a brilliant scientist named Sabrina Kaur. She was director of the Chrysalis project, sited in an underground facility in India's Thar desert. Project scientists attempted to improve the human genome and the breeding of men and women. Kaur donated her egg to be fertilized, carried it in a full term pregnancy, and gave birth to Kahn. The project results showed twofold increases in intelligence and fivefold strength increases over a baseline human. These top scientists conspired to create this super race in hopes that they would eventually command and or take control of Earth.
Unfortunately for the world, they succeeded. Khan led the project offspring in an attempt at world domination. During the Eugenic Wars, from 1992-1996, he was ruler of nearly a quarter of the Earth. At wars' end, Khan and many of his followers escaped in the SS Botany Bay, in suspended animation, traveling at sublight speeds. They were discovered in the Mutara sector in 2267 by the U.S.S. Enterprise, captained by James Kirk.
Kirk and an away team including historian Marla McGivers went aboard the Botany Bay and revived Khan, unaware of his involvement in the Eugenics Wars. Khan studied ship records, quickly bringing himself up to speed on 271 years worth of technological innovation. He then revived his own people and captured the crew of the Enterprise. The crew regained control of the ship and Kirk left Khan to rule on the abandoned planet Ceti Alpha V with 71 followers and McGivers, who became his beloved wife.
Khan was created for the original series Star Trek episode "Space Seed", and was named in honor of Gene Roddenberry's friend from World War II, Kim Noonien Singh. Roddenberry hoped his friend would hear his name on television and contact him, but never heard from Mr. Singh.
From an indomitable leader of the Augments in the Eugenics Wars, Khan was forced to feign compliance when revived aboard a strange ship centuries after launching from Earth. He used his charisma and tactical genius to charm McGivers into betraying the Enterprise. Following a loss to Captain Kirk in single combat, Khan was once again compliant in accepting exile.
But the new colony was on Ceti Alpha V for only a few months when Ceti Alpha VI exploded, shifting the orbit of Ceti Alpha V and killing many of Khan's people. With the loss of most life on the planet, except the Ceti eels, Khan's indomitable will reemerged. The eels took 20 of his followers, including his beloved wife. Fourteen years later, the U.S.S. Reliant went down to what they thought was Ceti Alpha VI, only to find out that due to the planet's shift they were really on Ceti Alpha V.
Khan and his people quickly captured Captain Clark Terrell and First Officer Pavel Chekov. The eels were dropped into their ears, affecting the cerebral cortex to allow them to become obedient to suggestion by Khan. He used them to capture the Reliant and strand its crew on the planet, returning to his merciless beginnings as leader. Kirk, now an Admiral, was left with a skeleton crew of trainees to investigate. Khan had the Reliant feign communications problems, allowing him to approach and fire on the unshielded Enterprise.
Khan gave Kirk five minutes to inform his crew that they must unconditionally surrender. Kirk used the Reliant's prefix code to override their shields and fire back. Khan now had to flee, his ship limping away as Kirk beamed to the center of the Genesis planet. Khan's suggestion triggered Captain Terrell and Commander Chekov to transport the Genesis device up to Khan's ship. Once Terrell was ordered to kill Kirk and refused, vaporizing himself with his own phaser to avoid murdering a fellow officer, Khan decided to maroon Kirk on the planet, leaving him with these words:
"I've done far worse than kill you...I've hurt you. And I wish to go on hurting you. I shall leave you as you left me – as you left her – marooned for all eternity at the center of a dead planet. Buried alive...buried alive!"
But following another ruse, Kirk and the rest of his party were beamed back up to the ship and fled toward the Mutara Nebula. Kirk taunted him, and Khan once again let his anger get the better of him in his quest for revenge. He pursued Kirk into the Nebula, losing track only to be overtaken and fired on. The ship nearly destroyed, a dying Khan activated the Genesis Device. He perished in an explosion of creative force that failed to reach the escaping Enterprise, delivering his last words, from Melville's Moby Dick as he did so:
"From Hell's heart, I stab at thee... For hate's sake, I spit my last breath at thee..."
Star Trek Into Darkness
Khan's origin remains the same in the alternate timeline, but he is revived Admiral Alexander Marcus of the Federation to construct weapons and warships for an upcoming war with the Klingon Empire.
Khan would rebel against Starfleet conduct acts of terrorism, one of which included the murder of Admiral Christopher Pike. The Enterprise crew captures him on Kronos, and he reveals the truth about his motives to them. Khan then works alongside Captain Kirk to arrest Marcus for his crimes only to betray Kirk, kill Marcus and attempt to destroy the Enterprise.
However, Khan rebels against Starfleet and kills Rear Admiral Christopher Pike among others in a series of terrorist attacks. The crew of the Enterprise captures him on Kronos, the Klingon homeworld, forcing him to reveal the truth about his past and Marcus' plan to wipe out his people. Khan assists Captain Kirk (Chris Pine) in an attempt to arrest Marcus, but betrays Kirk, kills Marcus, and capture the massive battleship, the USS Vengeance. Khan attempts to destroy the Enterprise, only to be tricked by Spock. He then attempts at another escape by sending the Vengeance into Starfleet’s base and San Francisco. Khan is eventually defeated in combat by Spock, who uses his blood and regenerative DNA to revive the deceased Kirk. He is then put back into cryogenic sleep along with his cohorts.