Warning: SPOILERS for Star Trek: Prodigy Season 1, Episode 11 - "Asylum"The whereabouts of Captain Chakotay (Robert Beltran) is one of Star Trek: Prodigy's biggest mysteries, and here are the possibilities of what could have happened to Admiral Kathryn Janeway's (Kate Mulgrew) closest friend. Janeway returned to the Delta Quadrant to search for Chakotay. Commanding the USS Dauntless, Janeway is in pursuit of the USS Protostar, of which Chakotay was originally the Captain. Janeway doesn't yet know the Protostar is now crewed by six alien teenagers, and they don't even know who Captain Chakotay really is, much less where he could be.
Star Trek: Prodigy established that Captain Chakotay launched the USS Protostar in 2383 with Admiral Janeway's blessing. Chakotay's mission was to return to the Delta Quadrant for an unstated purpose, but because the Protostar is equipped with a faster-than-warp Proto-Drive, he was supposed to make it back to Earth quickly after completing his assignment. However, the Protostar was found derelict on Tars Lamora by Dal R'El (Brett Gray) later in 2383. There was no sign of Chakotay or the Protostar's crew. Further, Star Trek: Prodigy later revealed that the Protostar has been moored on Tars Lamora since 2366 when the Diviner (John Noble) created his daughter, Gwyndala (Ella Purnell), because he was looking for the Starfleet ship at that time. Thus far, Chakotay has only appeared as a hologram and in flashbacks, and it's unclear if Admiral Janeway will find her friend or learn how and why Chakotay went missing.
Chakotay Is Dead In Star Trek: Prodigy
The most tragic possible outcome is that Captain Chakotay is dead. After all, there is no trace of him or the Protostar's crew, nor is it clear what happened to them. Chakotay may have lost his life keeping the Protostar safe from someone trying to steal the ship and its Proto-Drive. He may even have been disintegrated, which explains why there are no remains of Chakotay left behind. Obviously, it would be heartbreaking for Admiral Janeway to travel millions of miles to save Chakotay, only to find out he was already dead and there was nothing she could do.
Star Trek: Prodigy is a show aimed at younger audiences, but this doesn't mean that the series wouldn't kill off Chakotay. Star Trek may be about space adventure and exploration, but there's also a dark side to the franchise and major characters do die in the various Star Trek TV shows and movies. If Chakotay is dead, it would mainly impact the older viewers who know the Captain from Star Trek: Voyager. The younger Prodigy audience, like Dal, Gwyn, and their friends, mainly don't know who Chakotay is. While it's hard to believe that Star Trek: Prodigy would kill Chakotay instead of positioning his rescue for a happy ending, it's still a possibility that must be considered.
Chakotay Time Traveled And Isn't In Prodigy's Era
Chakotay may not actually be in Star Trek: Prodigy's era circa 2383. The former Maquis Captain may have launched the Protostar in that year, but the starship is capable of time travel via the Proto-Drive. After all, it somehow ended up in 2366, and the Diviner, who also time-traveled back from 50 years in the future, was searching for the Protostar even then. It's possible the Protostar time traveled 50 years forward, perhaps accidentally, and Chakotay may have made contact with the Diviner's homeworld of Solum.
The Vau'Nakat suffered a planetary tragedy that devastated Solum, and the Diviner blames Starfleet and the Federation for what happened to his homeworld. Star Trek: Prodigy may reveal that Captain Chakotay went to the future. He may be trapped on Solum, but Chakotay sent the Protostar back in time, and it arrived in 2366. (The Diviner also time traveled and landed even farther back in time than 2366 because he was searching for the Protostar for years before Gwyn was born). Wherever Chakotay is, it simply may not be in the same timeline as Admiral Janeway.
Chakotay Is A Prisoner In Star Trek: Prodigy (Or Assimilated)
Chakotay may be someone's prisoner during Star Trek: Prodigy, and possibly so is the Protostar's crew. After all, Chakotay and the USS Voyager made a number of enemies in the Delta Quadrant during the seven years they journeyed back to Earth. Any number of hostile Delta Quadrant denizens, including the Kazon, could have captured Chakotay, but not his starship. The Borg is also appearing in Star Trek: Prodigy season 1, and the cybernetic race not only hails from the Delta Quadrant but also have an enmity with the USS Voyager. If Chakotay is a prisoner, Admiral Janeway is just the person to set him free. And if Chakotay was assimilated by the Borg, Janeway also has experience in reclaiming Borg and returning their humanity, just like Seven of Nine (Jeri Ryan) on Star Trek: Voyager.
Chakotay Is In Hiding In Star Trek: Prodigy
The final possibility is Chakotay is in hiding in Star Trek: Prodigy. Whatever happened to the Protostar could have motivated Chakotay to conceal his identity so that he's somewhere in the Delta Quadrant and doesn't wish to be found. Chakotay may even be hiding somewhere in plain sight if he's using holographic technology to alter his appearance. If this is the case, it would be fascinating to find out what would cause Chakotay to hide and give up the USS Protostar, but it would also still beg the question of what happened to his crew.
Star Trek: Prodigy Season 1 is streaming on Paramount+.