Star Trek: 10 Starships That Went Missing
2. Bonaventure
The Bonaventure disappeared 'sometime before the 2260s,' according to Spock in The Animated Series episode The Time Trap. Starfleet lost all record of the ship once it entered the Delta Triangle, a region of space in the Beta Quadrant where Kessik, Bellatrix, and FGC-82659 met. The Star Trek: Star Charts and Stellar Cartography: The Starfleet Reference Library both state that the ship was lost there in 2079.
When the Enterprise is forced into this region following an attack by Kor, Scotty marvels at the Bonaventure's appearance. He claims that it was the first starship given a warp drive, though, of course, it couldn't be the first ship with one. Zefram Cochrane's Phoenix took that honour, while the Bonaventure may have been one of the first.
Though the Enterprise escaped the Delta Triangle, the Bonaventure remained behind. There it would stay for at least another one hundred years until, according to IDW's Star Trek: Lower Decks debut comic book, it was re-discovered in normal space by the USS Cerritos.