Star Trek has finally revealed what happened to Chakotay after Star Trek: Voyager. SPOILERS follow for the Star Trek: Prodigy episode "Preludes." Chakotay returns in Star Trek: Prodigy, voiced by Robert Beltran, the same actor who played the former Maquis agent turned USS Voyager's first officer in Star Trek: Voyager. While Star Trek: Prodigy has previously offered a clue about what became of Chakotay and his crew aboard the USS Protostar, discovering their fates has remained the primary motivation of Vice Admiral Janeway's pursuit of the ship and its unusual crew. While that mystery remains in place for Janeway, Prodigy viewers now know what became of Chakotay.
The revelation comes couched in another revealing Ensign Asencia, who serves under Janeway aboard the USS Dauntless, is a mole within Starfleet. The character, voiced by Jameela Jamil, is secretly The Vindicator. She is a Vau N'Akat, like the show's primary antagonist, The Diviner. As The Diviner struggles to remember who he is, The Vindicator takes the opportunity to refresh his memory, revealing what became of Chakotay and his crew in the process.
The Diviner and The Vindicator come from Solum, a planet deep in the Delta Quadrant. Despite being technologically advanced, the Vau N'Akat remained isolated, believing themselves the only intelligent beings in the universe. Starfleet's arrival at a date in the future changed all that, leading to infighting among the Vau N'Akat over how to respond to Starfleet's invitation to join the galactic community. The fighting left Solum in ruins and the Vau N'Akat with no means of reprisal.
That changed when a temporal anomaly appeared over Solum. Chakotay had taken the experimental Protostar ship into the Delta Quadrant to help chart the region of space under better circumstances than during his original trip aboard Voyager. However, the Protostar encountered the temporal anomaly that flung the ship forward in time, arriving at Solum after its fall. Chakotay and crew become prisoners while the Vau N'Akat survivors devise a plan to travel back in time with the Protostar and destroy Starfleet before it can make first contact.
However, Chakotay managed to lead a prison break, allowing him and his crew to send the Protostar safely back through time into the past without the Vau N'Akat. Following this, the Vau N'Akat formed the Order, a group dedicated to traveling back through time to find the Protostar and the secret weapon the Vau N'Akat installed onboard to destroy Starfleet. The Diviner and the Vindicator are members of the Order, though they arrived decades apart due to the temporal anomaly's collapse during transit.
The anomaly's collapse also means Chakotay and his crew remain stranded on Solum in the future. What this means for Janeway's search will presumably be revealed as Star Trek: Prodigy continues.
Star Trek: Prodigy debuts new episodes on Thursdays on Paramount+. Star Trek: Voyager is streaming now on Paramount+.