(covers information from several alternate timelines)
The SS Botany Bay was a DY-100-class sleeper ship built on Earth in the late 20th century. The Botany Bay was launched from Earth in 1996, under the command of Khan Noonien Singh. The Botany Bay was used by a group of genetically-enhanced Humans known as 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 eighty-four of his followers were placed in cryogenic freeze. Twelve of the suspended animation life support canisters failed while in deep space, leaving Khan himself and seventy-two 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 doubted the theory of the ship's existence. Malik used it as an example of why the Augments Soong created should not run away. (ENT: "The Augments")
In 2267, 271 years after its launch, the Botany Bay was discovered by the USS Enterprise in a sector that was infrequently visited by Earth ships. The Botany Bay was rigged for towing by crew from the Enterprise. Traveling at warp factor 2, the Enterprise, with the Botany Bay traveling alongside, entered the adjacent Sector 25712 on a heading toward the sector's command base – Starbase 12.
Upon revival, Khan and his followers, with the assistance of Lieutenant 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 eighteen 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 Commander John Harrison. (Star Trek Into Darkness)
Eighty-five Augments were placed in cryogenic freeze. Twelve of the suspended animation life support canisters failed leaving thirty female and forty-three 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)
|DY-100: SS Botany Bay|
|DY-245: SS Hatteras • DY-430: SS Urusei Yatsura|
|DY-500: SS Mariposa · HMS Lord Nelson (DY-500-B) · SS Hokule'a (DY-500-C)|
|DY-732: VK Yuri Gagarin · HMS New Zealand (DY-732 [N])|
|DY-950: DEV Eagle Valley • DY-1200: VK Velikan|
The original model was designed by Matt Jefferies, and most likely built by Film Effects of Hollywood. The model stood 44 inches in length, and was constructed of wood, with no internal lighting. Jefferies 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 was 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's (DS9: "Dax") quarters or Varis Sul's (DS9: "The Storyteller") and Vash's guests quarters (DS9: "Q-Less") on Deep Space 9) was 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".
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 Two, the Botany Bay was launched from Earth on January 11, 1996.
In contrast to that, in the comic miniseries Star Trek: Khan, Khan from the alternate reality claims that the Botany Bay launched sometime after May 6, 1996.
According to the Star Trek Encyclopedia (4th ed., vol. 1, p. 98), "A conjectural model of the Botany Bay, built by Greg Jein for a photograph in the Star Trek Chronology, was equipped with several space shuttle-style solid rocket strap-on boosters, suggesting how the 1996-vintage spacecraft might have gotten into orbit. The model was seen as a desktop decoration in Rain Robinson's SETI laboratory in the 1996 scenes of "Future's End" and "Future's End, Part II" (VOY) and the photograph was used as set dressing on the wall of the 602 Club in "First Flight" (ENT)."
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 orbiter. The "launch mode" model was built by Greg Jein, while Michael Okuda composited the image, using a NASA photo of a space shuttle launch.
The Starships RPG sourcebook gives the Botany Bay's registry as DY-109.