Kirk assembles a boarding party, consisting of himself, McCoy, Scotty, and the ship’s historian, Lieutenant Marla McGivers. As they prepare to beam over, Scotty observes that the ship’s life support systems are coming back online. Once aboard, Scotty confirms that the Botany Bay is an Earth vessel and McGivers identifies it as a sleeper ship, designed to keep its crew in stasis for lengthy interplanetary voyages. Suddenly, one of the stasis chambers activates, beginning the process of reviving its occupant, likely the leader. The unit malfunctions, nearly killing the man inside, though Kirk manages to break the glass and the man wakes briefly. Kirk sends him back to the Enterprise with McCoy and McGivers is clearly awestruck.

Scotty finds that several of the Botany Bay’s life support canisters have failed. leaving a total of seventy-two survivors. With the ship in tow, the Enterprise heads for Starbase 12. In sickbay, the twentieth-century man regains consciousness, avails himself of a scalpel, and threatens McCoy with it upon his return. After a tense moment, he returns the scalpel and McCoy summons Kirk. The man evasively identifies himself simply as “Khan”, claiming to have been an engineer of sorts.

Rather than elaborate on his history, Khan claims fatigue. He also asks and is granted access to the ship’s technical manuals. Later, Khan becomes acquainted with McGivers and her infatuation becomes increasingly obvious. Later still, the crew hosts Khan at a banquet in the officer’s mess, McGivers’ idea of a “Welcome to the twenty-third century” party. The banquet quickly descends into a sort of verbal sparring match between Khan and Spock, eventually revealing that his sympathies during the Eugenics Wars were with the tyrants. After this, he again claims fatigue and returns to his quarters. McGivers visits to apologize and Khan’s dark side is revealed as he declares his intention to take control of the Enterprise and browbeats McGivers into pledging herself to him.

The senior staff gathers for a meeting where Spock confirms the identity of their guest: Khan Noonien Singh. Not merely sympathetic to the tyrants, he is in fact one of the genetically engineered supermen who seized power on Earth in the late twentieth century. He was also the last to be overthrown, at one point acting as absolute ruler of more than a quarter of the planet, controlling territory from Asia to the Middle East. After the briefing, Kirk visits Khan in his quarters, which are now locked and under guard.

With the masks now off, Khan tells Kirk that he and his followers left Earth in search of a new life and a chance to build a new world. He condescendingly remarks on how little mankind has changed and suggests that he and his fellow augments will do quite well in this century.

Once Kirk leaves, Khan breaks out of his quarters and incapacitates the guard while McGivers takes control of the transporter room. By the time the Starfleet crew realizes what is happening, Khan has returned to the ship with his revived followers and taken control of engineering. From there, he contacts the bridge, telling Kirk that he has cut off life support and demanding his surrender.