Star Trek: Lower Decks season 3 revealed the answer to a big question about the Captain of the USS Enterprise. The USS Enterprise-E briefly returned in Star Trek: Lower Decks' explosive series finale, but the flagship of the United Federation of Planets does not arrive in time to save the day. Nor did "The New Next Generation" show the Enterprise's Captain or crew. While this might seem like Star Trek: Lower Decks leaves the question about who is in command of the Enterprise-E up in the air, the show actually answered that question two seasons ago.
When a massive and unstable quantum fissure threatens to destroy Star Trek's entire Prime Universe in Star Trek: Lower Decks' finale, Starfleet has no choice but to rely on the USS Cerritos. In the end, the Cerritos crew rallies together and saves the universe by stabilizing the quantum fissure. In the final scenes of the finale, several Starfleet ships are docked at Starbase 80, including the USS Enterprise-E. Star Trek: Lower Decks never shows the ship's crew, although the show has already made clear that Captain Worf (Michael Dorn) should be in command at this point in the Star Trek timeline.
In the Star Trek: Lower Decks season 3 finale, Beckett Mariner briefly joins the Independent Archaeologists Guild alongside Petra Aberdeen (Georgia King). Mariner soon grows uncomfortable not knowing where Petra's funding is coming from and confronts her. Petra reveals that her benefactor is none other than Admiral Jean-Luc Picard. This confirms that Picard has already become Admiral by 2381, meaning that Captain Worf (Michael Dorn) would be in command of the USS Enterprise-E by the time of Star Trek: Lower Decks series finale in 2382.
Star Trek: Lower Decks Season 3 Revealed Picard Is Already An Admiral
Worf Has Still Never Been Seen On Screen As Captain Of The Enterprise
Captain Jean-Luc Picard (Patrick Stewart) took over command of the USS Enterprise-D in 2363 at the beginning of Star Trek: The Next Generation, and remained captain until that ship's destruction in 2371 in Star Trek Generations. Picard then became Captain of the USS Enterprise-E for Star Trek: First Contact, Star Trek: Insurrection, and Star Trek: Nemesis. Commander William Riker (Jonathan Frakes) became Captain of the USS Titan in Nemesis while Picard remained in command of the Enterprise. Picard was promoted to Admiral sometime in 2381, as revealed in Star Trek: Lower Decks season 3, episode 10, "The Stars At Night."
What Happens To The USS Enterprise-E After Star Trek: Lower Decks’ Finale
Whatever Happened To The Enterprise-E Was Not Worf's Fault
While very little has been revealed about Captain Worf's tenure in command of the USS Enterprise-E, Star Trek: Picard season 3 offered a hint about the ship's ultimate fate. In Picard season 3, episode 9, "Vox," Commodore Geordi La Forge (LeVar Burton) reveals that he has spent the last twenty years rebuilding the USS Enterprise-D. As Admiral Picard and his crew admire their former ship, La Forge points out that they "obviously can't use the Enterprise-E." Worf promptly responds with, "that was not my fault," implying that the ship was destroyed or somehow lost while Worf was in command.
Star Trek: Picard season 3 takes place in 2401, meaning about twenty years have passed since the events of Star Trek: Lower Decks' final season. Worf appears to have been working on his own for a while by the time of Picard season 3 and is a "subcontractor" for Starfleet Intelligence in 2401. This suggests that Worf's time in command of the Enterprise may have been relatively brief before the event that destroyed the ship. Hopefully, a future Star Trek project will offer more insight into the fate of the Enterprise-E or even show Captain Worf in command after Star Trek: Lower Decks.