The Botany Bay was used by a group of genetically-enhanced Humans (Augments), led by Khan Noonien Singh, in an attempt to escape from Earth after being defeated by non-Augments. Khan intended to find a world for himself and his people that they could colonize. 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. This left Khan and 72 Augments to survive. (TOS: "Space Seed"; Star Trek II: The Wrath of Khan)
During the 22nd century, the Botany Bay was believed to be a myth. Arik Soong, an ancestor of Noonian Soong, was among those who believed this. Malik used it as an example of why the Augments Soong created should not run away. (ENT: "The Augments")
Upon revival, Khan and his followers, with the assistance of Lt. Marla McGivers, seized control of the Enterprise, and left the now-useless Botany Bay adrift in space. The hijacking 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-issue cargo carriers provided by the Enterprise to start the colony. The cargo carriers 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)
In 2258 of the alternate reality, Section 31 performed secret investigations in unexplored space for means of better defending the Federation after the destruction of Vulcan. They discovered the Botany Bay, 262 years after launch, and Khan was awoken. With the other 72 augments still in stasis under Section 31's control, he was forced to join and work for Starfleet as John Harrison. (Star Trek Into Darkness)
85 Augments were placed in cryogenic freeze. Twelve of the suspended animation life support canisters failed leaving 30 female and 43 male Augments to survive, including Khan, Otto, Joaquin, Kati, Rodriguez, Ling, McPherson, and others. Lieutenant Commander Montgomery Scott described them as a group of mixed types: Western, mid-European, Latin, Oriental. (TOS: "Space Seed"; Star Trek II: The Wrath of Khan)
- The Botany Bay was named for the Australian geographical location, the site of the first penal colony on the shores of Australia.
- The original model was designed by Matt Jefferies, and most likely built by Film Effects of Hollywood. The model stood 44" in length, and was constructed of wood, with no internal lighting. Jeffries also added the weathering seen on the model. Effects shots showing the Botany Bay alongside the Enterprise were filmed at Film Effects. (Star Trek Magazine issue 120)
- Based on behind-the-scenes photos from The Wrath of Khan, Khan's shelter in the film consisted of Starfleet cargo containers. They were designed based on the cargo containers hauled by CMUs in Star Trek: The Motion Picture, complete with an attachment sled. The movie-era Federation seal can also be seen on the exterior of one of the containers and is just barely visible in the film itself.(citation needed • edit)
- In the 2006 "remastered" version of "Space Seed", the Botany Bay appeared adrift on a different axis than the Enterprise in a much more "weathered" state than it did in its original appearance, to match Spock's line stating that its "hull surface is pitted with meteor scars." The conning tower was also given a very small docking port, added by Michael Okuda at the suggestion of a NASA engineer with the thought that a spacecraft built in the 1990s would have such a port to dock with the International Space Station.
- The Bajoran religious wheel symbol (sometimes seen, for example, in Kira's, Sisko's, and Dax' (DS9: "Dax") quarters or Varis Sul's (DS9: "The Storyteller") and Vash's guests quarters (DS9: "Q-Less") on Deep Space 9) is composed of rotated images of the Botany Bay. A more prominently featured version can be seen in Kai Winn's quarters during her meditation in "'Til Death Do Us Part".
- Star Trek: Star Charts places the border of the sector where the Botany Bay was found twenty light years away from Earth.
- During the production of Star Trek it was briefly considered putting a shot of the Botany Bay in after the end credits, as an Easter egg. However, it was decided against, as it was felt that this would tie the hands of the production staff for the film's sequel story. (Star Trek audio commentary)
- According to the novel The Rise and Fall of Khan Noonien Singh, Volume 2, the Botany Bay was launched from Earth on January 11, 1996.
- The second edition of the Star Trek Chronology featured an image of the Botany Bay being launched from Earth with the use of booster rockets similar to those used by the Space shuttle. The "launch mode" model was built by Greg Jein, while Michael Okuda composited the image, using a NASA photo of a space shuttle launch.