WARNING: This article contains SPOILERS for Star Trek: Prodigy season 2
Summary
Captain Chakotay (Robert Beltran) finally gets theStar Trek: Voyagerreward he always deserved at the end ofStar Trek: Prodigyseason 2.Admiral Kathryn Janeway (Kate Mulgrew) spends the better part ofStar Trek: Prodigyseason 1 searching for Chakotay and the USS Protostar, and finds a ragtag group of Delta Quadrant kids crewing the Protostar instead her former First Officer. InStar Trek: Prodigyseason 2, Dal R’El (Brett Gray), Gwyndala (Ella Purnell), Rok-Tahk (Rylee Alazraqui), Jankom Pog (Jason Mantzoukas), Zero (Angus Imrie), and Murf (Dee Bradley Baker) become Starfleet Academy hopefuls, taken under Admiral Janeway’s wing aboard theLamarr-class USS Voyager-A.
InStar Trek: Voyager, Chakotay was the Captain of the Maquis raider ValJean, which was taken to the Delta Quadrant along with the USS Voyager.Captain Janeway smartly made Chakotay Voyager’s First Officer with the field rank of Commander, commensurate with Chakotay’s previous experience in Starfleet. Putting Chakotay in a position of power ensured that the Maquis would continue to respect the chain of command on a Starfleet ship. Seeing the USS Voyager home to the Alpha Quadrant means that Chakotay earns back his original Starfleet rank. BeforeStar Trek: Prodigy,Chakotay is promoted to Starfleet Captain, and commands theoriginal USS Protostarwhen it disappears in 2382.

Star Trek: Prodigy Season 2 Ending & Shocking Season 3 Set Up Explained
Star Trek: Prodigy season 2 brings the time travel saga of the USS Protostar full circle. Here’s what happened and what it all means for season 3.
Chakotay Finally Becomes USS Voyager-A’s Captain In Star Trek: Prodigy Season 2
Prodigy’s Ending Makes Chakotay Captain Of Voyager At Last
At the end ofStar Trek: Prodigyseason 2, Chakotay finally becomes Captain of the USS Voyager-A. Admiral Janeway’s search for Chakotay is stymied by Admiral Edward Jellico (Ronnie Cox), so Dal and the would-be cadets of the Voyager-A take the mission into their own hands. Time-travel shenanigans and the intervention of Traveler Wesley Crusher (Wil Wheaton),Star Trek’s original prodigy-turned-Traveler who’s determined to set theStar Trektimelineright, eventually lead theProdigykids right to Chakotay.Captain Chakotay becomes theStar Trek: Voyagercharacter with the spotlight inStar Trek: Prodigyseason 2, as the kids rehabilitate both the USS Protostar and Chakotay himself, and bring both home.
Janeway’s priority always remained squarely on finding Chakotay.
Captain Chakotay’s reunion with Admiral Janeway is just the precursor to a new dynamic forJaneway and Chakotay’s relationship. It’s not hard to believe that the mission to locate Captain Chakotay was always going to be Janeway’s last, given the way that Janeway and Jellico were consistently at odds throughoutStar Trek: Prodigyseason 2, and Janeway’s priority always remained squarely on finding Chakotay. With Chakotay found,Admiral Janeway decides it’s time to retire to a farmhouse in her home state of Indiana, and leaves the Captain’s chair of Voyager-A openfor Chakotay as his new command.
Janeway’s First Officer on the USS Dauntless and USS Voyager-A, Commander Tysess (Daveed Diggs), was one potential choice to take up command of Voyager-A, but in the end, it has to be Captain Chakotay.

Why Chakotay Deserved To Be Captain Of Voyager After Janeway
Captain Chakotay Proves He’s Earned Command Of Voyager’s Legacy
Despite Captain Chakotay’s checkered history with Starfleet, his Maquis past is long behind him, andChakotay has proven that he deserves command of the USS Voyager-A after Admiral Janeway’s retirement. In the future, Chakotay learns about theVau N’Akat’s Living Constructweapon inside the USS Protostar, which will decimate the United Federation of Planets from the inside if the Protostar comes into contact with any Federation ships. Even a distress beacon will put the Federation at risk, so Chakotay chooses to remain in self-imposed exile for ten years to protect Starfleet and the Federation. And that’s just the start of Chakotay’sStar Trek: Prodigyarc.
It’s fitting that the position of Voyager’s new captain goes to Captain Chakotay.Admiral Janeway trusts Chakotay with the legacy of the USS Voyager namebecause they brought the first Voyager home together. The ill-fated journeys of the ValJean, USS Voyager, and USS Protostar pushed Chakotay to his limits, testing Chakotay’s loyalty and mettle. After hitting rock bottom and being helped up again by Janeway’sStar Trek: Prodigycadets, Chakotay ultimately comes to the other side of his adventures through the Delta Quadrant, through time, and acrossStar Trek’s alternate universes. The perfect reward for Captain Chakotay’s incredible journey is becoming Captain of the USS Voyager-A.
