The ship was lost on her third mission, in the Delta Triangle, several decades before 2269. The ship encountered a time warp vortex and became trapped inside Elysia, a small alternate universe, a parallel time continuum, that periodically touched the prime universe in the Delta Triangle region. In Elysia, the Bonaventure remained adrift along with a large number of other ships unable to escape.
The Bonaventure may have been named after the Bonaventure (C1-21). There have been several ships in the Royal Navy with the name HMS Bonaventure. A Royal Navy aircraft carrier, HMS Powerful, was renamed HMCS Bonaventure by the Royal Canadian Navy in 1952.
It is not clear if the Bonaventure was a ship launched by United Earth Space Probe Agency or Starfleet, or another agency. It is equally unclear if she was launched in the 21st, 22nd, or 23rd century. To truly be the first starship with warp drive, she would have had to be launched before the SS Valiant was launched in 2065 and after the launch of the Phoenix in 2063. The undeveloped Star Trek: The First Adventure movie was to feature the first dilithium-powered warp test ships in the 23rd century, called the Bonaventure and Bonaventure II, a new technology Montgomery Scott and George Kirk worked on.
Star Trek: Star Charts, on page 64, names the ship as SS Bonaventure and lists the year she was lost in the Delta Triangle, over 200 light years away from Earth, as 2079. This date would be consistent with the fact that a Human female was a member of the Elysian Council where everyone was stated to be several centuries old. The Bonaventure's 23rd century design features are however somewhat inconsistent with early Earth starship design, as it was later on depicted in Star Trek: Enterprise.
There is also a Bonaventure listed in the Star Trek Spaceflight Chronology. It looks totally different from both this vessel and the Bonaventure (C1-21). The UNSS Bonaventure was a Warp 2.5 Cruiser of the Cochrane Class under the command of Captain Hadrian Huckleby. She was was Earth's first Warp Drive ship. The UNSS Bonaventure began Earth's Warp Drive era with a trip to Tau Ceti four years after the first successful demonstration of warp technology. She was unaccountably lost on her third mission, 18 years later, on the voyage to Sirius. The UNSS Bonaventure was stated to have a maximum emergency velocity of Warp 2.5, although engines experienced a slight power breakdown at that speed. The Bonaventure was also the first Earth ship to use alien technology as the warp guidance system. A ship passing Warp 2 this early is inconsistent with what is established in ENT: "First Flight".
A 2006 Star Trek calendar depicted a vessel with the registry number NCC-1000 that would later be identified in the Ships of the Line art book as a Bonaventure-class vessel.