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The Starship Enterprise discovers a ship floating in space, seemingly abandoned. Later identified as the S.S. Botany Bay, the Enterprise sends over a landing party, and discover it is a converted sleeper ship, launched from Earth sometime during the 1990's. They manage to revive some of the people in cryogenic suspension, among them the warlord Khan Noonien Singh (played by guest star Ricardo Montalban).
It transpires that after the Eugenics War on Earth and the defeat of the genetically enhanced faction which had tried to seize control of the world, its leader, Khan, and his closest followers stole an experimental sleeper ship and set out on it. After Khan is revived, he attempts to seize control of the Enterprise, but is foiled by Captain James T. Kirk. It is eventually decided to exile Khan and his group to an uncolonised planet, along with the ship's historian, who had fallen in love with him.
The story is continued in the feature film Star Trek II: The Wrath of Khan.