The SS Botany Bay was a DY-100-class sleeper ship launched in 1996.

The Botany Bay was used by a group of genetically-enhanced Humans, led by Khan Noonien Singh, to leave Earth. Initially Khan and 84 of his followers were placed in cryogenic freeze. Twelve of the suspended animation life support canisters failed while in deep space.

During the 22nd century, the Botany Bay was believed to be a myth, even by Arik Soong. Malik used it as an example of why the Augments Soong created should not run away.

In 2267, 271 years after launch, the Botany Bay was discovered by the USS Enterprise. She was adrift in a sector where Starbase 12 was the command base for Federation Starfleet vessels.

Upon revival, Khan and his followers, with the assistance of Lt. Marla McGivers, seized control of the Enterprise. The hijack was quickly overcome by Captain Kirk and his officers. Kirk offered Khan, his followers, and Marla McGivers the chance to settle the uninhabited world of Ceti Alpha V, an offer which Khan accepted. (TOS: "Space Seed")

Various personal effects transferred from the Botany Bay were kept within Starfleet cargo carriers. They were subsequently used as shelters by Khan and his followers for almost fifteen years on Ceti Alpha V after the planet became a desert wasteland. (Star Trek II: The Wrath of Khan)

The Botany Bay was named for the Australian geographical location, the site of James Cook's first landing in 1770 and, later, a famous penal colony on the shores of Australia.