Nuclear-powered vessel of the DY-100 class, which was Earth's standard interplanetary transport of the late 20th century. Named after an infamous Australian penal colony, the S.S. Botany Bay was converted into a "sleeper ship" and launched in 1996 with refugees from the Eugenics Wars, namely Khan Noonien Singh and his band of genetically-bred "supermen." The launch was kept secret in order to not alarm a war-weary population that the tyrant who controlled more than one-fourth of the planet from 1992-96 was still alive. After being defeated in Earth's Eugenics Wars, Khan and his followers hoped to find another world to conquer and rule.

The Botany Bay drifted in space for over two centuries with its passengers in suspended animation, until the U.S.S. Enterprise discovered the sleeper ship near the Mutara Sector in 2267. The ship's automatic systems attempted to revive Khan first — being the leader of the group — but malfunctioned in the process, forcing the Enterprise crew to intervene and save the historical figure. Captain Kirk intended to keep the other passengers in stasis until the Enterprise reached Starbase 12 with the Botany Bay in tow, but Khan defied security and transported back to the sleeper ship to revive his crewmates to begin an insurgency. Of the 84 original passengers, 72 survived, 30 of them women. The Botany Bay was discarded in deep space when Khan attempted to commandeer the Enterprise, but a variety of belongings were retained (such as a collection of classic books and a seatbelt) which found their way to Ceti Alpha V, where Khan and his people were eventually exiled.