Khan awakened from the Botany Bay

In 2267 the Enterprise came across the SS Botany Bay, an old Earth sleeper ship from the late 20th century, drifting in space. Aboard, about seventy people lay in suspended animation. Their leader, revived first, introduced himself simply as Khan, but was soon identified as Khan Noonien Singh, a genetically engineered superhuman who had once ruled a vast part of Earth during the Eugenics Wars before fleeing into space.

Charismatic and ruthless, Khan won over the ship's historian, Lieutenant Marla McGivers, revived his followers and seized control of the Enterprise, threatening to kill Kirk unless the crew obeyed. With McGivers' last-minute help, Kirk regained his ship and overpowered Khan.

Rather than imprison them, Kirk exiled Khan and his people to the untamed world of Ceti Alpha V, where McGivers chose to join him. The decision had grave consequences: some months later a nearby planet exploded, devastating the colony, and when Khan was found again in 2285 he blamed Kirk for the death of many of his followers, setting the stage for The Wrath of Khan.