The Enterprise discovers the S.S. Botany Bay, an old-style, pre-warp sleeper ship from Earth that contains several bodies in stasis. Amongst these bodies is Khan Noonien Singh, a genetically-engineered strongman and one of the great leaders of Earth's Eugenics War of the 1990s. Once aboard the U.S.S. Enterprise, Khan quickly befriends the beautiful Lieutenant Marla McGivers, and together with his Botany Bay crew and new companion, they seize control of the Enterprise.

Ricardo Montalban (Khan Noonien Singh)
Madlyn Rhue (Lt. Marla McGivers)
DeForest Kelley (Dr. Leonard H. McCoy)
James Doohan (Lt. Cmdr. Montgomery Scott)
Blaisdell Makee (Lt. Spinelli)
Nichelle Nichols (Lt. Uhura)
Mark Tobin (Joaquin)
Kathy Ahart (Crew Woman)
John Winston (Lt. Kyle)

• The S.S. Botany Bay is a DY100-class vessel built in the 1990s.
  
• Khan and his crew are exiled to planet Ceti Alpha V where they must start life anew. Rather than face court martial, Marla McGivers chooses exile with Khan. (Female officers don't seem to fare very well in The Original Series.)
  
• Spock wonders what will become of the seed they have planted. These events become the background for the motion picture Star Trek II: The Wrath of Khan.