Khan Noonian Singh
Ricardo Montalban

Lt. Marla McGivers
Madlyn Rhue

Lt. Spinelli
Blaisdell Makee

Joaquin
Mark Towbin

Transporter Chief Kyle
John Winston

The Enterprise investigates old-fashioned Morse code signals it has received and finds that they are coming from an ancient vessel of the DY-100 class. Despite the age of the ship, sensors indicate that some equipment is still functioning and that there are faint life signs aboard. The ship is identified as the 'Botany Bay', which would have been launched during Earth's Eugenic Wars, but no details exist in the computer databanks.

Following McCoy's report that there are possibly sixty or more bodies on board, Kirk beams aboard with McCoy, Scotty and a historian called Marla McGivers where they discover that it is a 'sleeper' ship and its crew are in suspended animation. Scotty brings the main power back online and one of the sleepers start to wake. Despite an equipment failure the sleeper is saved and the rest of the ship's inhabitants are taken on board the Enterprise where 72 of the 84 'crew' prove capable of being revived.

Spock has become interested in the ship's purpose as it was launched during a World War with nowhere to go and virtually no chance of survival. McCoy advises Kirk that the first sleeper is genetically modified to be much stronger and more intelligent than ordinary humans of the time. The man, named Khan Noonien Singh, is given access to ship's engineering manuals during his recovery but skilfully hides his true identity until Spock discovers that he was one of a number of genetically engineered tyrants who escaped justice after the Eugenics Wars and were never traced.

The rest of the genetically modified sleepers awake and, with the help of Marla McGivers who has become infatuated with Khan, take over control of the ship. It becomes increasingly obvious to Marla that Khan is not as 'nice' as he pretends and when he threatens to kill Spock and Kirk to force the rest of the crew to obey him she sees the error of her ways and assists in plotting his defeat. Khan takes refuge in engineering and sets the engines to overload. Kirk pursues him and manages to subdue him in hand to hand combat despite Khan's superior strength.

Kirk holds a hearing aboard ship to lay charges against Khan and his people but agrees to 'maroon' them on the harsh desert planet Ceti Alpha V to give him and his followers the opportunity of creating a 'brave new world' for themselves. Faced with the alternative of court martial for mutiny, Marla McGivers opts to go with them. After transporting the last of them down, Spock passes comment that it would be interesting to return in a hundred years' time 'to see what springs from the seed' that Kirk has sown.

n.b. They didn't have to wait that long as events in the second Star Trek feature film 'Star Trek II - The Wrath Of Khan' have shown.