Star Trek: 10 Starships That Went Missing

4. USS Bozeman

The USS Bozeman had a longer life than most ships in Starfleet, though it took the shortest possible route to its destination. In 2278, just three weeks after departing Spacedock, this Souyz-class vessel vanished, becoming a mystery that would puzzle the Starfleet Corps of Engineers for almost a century to follow. 

The truth of what happened to the vessel is stranger than fiction. In the Typhon Expanse, it encountered a rift that flung it forward in time by 90 years. It also flung it directly into the starboard nacelle of the Enterprise-D (with a little help from the latter's transporter beam - thanks a lot, Data).

The resulting explosion destroyed the Galaxy-class ship but then locked both vessels into a temporal loop. For the Enterprise, this lasted days. For the Bozeman, it was decades. 

The Bozeman finally returned home, ship and crew intact, in 2368, where it re-entered service in Starfleet. It was still in active service by at least 2371, while a ship named Bozeman took part in the Battle of Sector 001 in 2373.