WARNING: The following contains spoilers for Star Trek: Prodigy Season 1, Episode 10, "A Moral Star, Part 2," streaming now on Paramount+.
For much of Star Trek: Prodigy, the animated series was largely set in the Delta and Gamma Quadrants, far outside of the jurisdiction of the United Federation of Planets and Starfleet. While familiar species and the legacy of the wider Star Trek Universe have certainly been felt throughout the course of the series -- especially through its stranded Starfleet vessel the USS Protostar -- Dal and his friends have largely enjoyed existing in their own corner of the galaxy. However, the Protostar itself could be the starship that dooms the entire Federation if the evil Diviner's master plan manages to succeed.
Possessing the experimental Proto Drive, powered by a nascent star in its engine core, the Protostar is potentially the fastest vessel in Starfleet's extensive armada. Originally commanded by Captain Chakotay, Kathryn Janeway's trusty first officer throughout Star Trek: Voyager, the ship was boarded by the Diviner's robotic right-hand man, Drednok. And though the Diviner lost control of the Protostar on the harsh mining planet of Tars Lamora for well over a decade in the interim, he still managed to implant a secret device on the starship that could completely dismantle Starfleet from within.
As Gwyn is poised to reclaim control of the Protostar from her twisted father, the Diviner reveals that he has implanted the Protostar with a device designed to infiltrate and corrupt the systems of any Starfleet vessels it encounters. This corruption results in the ships turning against each other, as well as the Federation's destruction at the hands of its vast fleet. However, though the Diviner is defeated and left behind on Tars Lamora, Gwyn's mind is wiped of this revelation, leaving her unaware of the danger that the Protostar possesses as the similarly oblivious Dal pilots it towards Federation space.
This certainly isn't the only time in Star Trek history that Starfleet vessels have been turned against the Federation. The Star Trek: The Original Series episode "The Ultimate Computer" saw a sentient program take control of the Enterprise and attack other starships with lethal results until Captain Kirk outsmarted it. The first season of Star Trek: Picard was shaped by Federation androids being taken over by a far-reaching Romulan conspiracy, devastating Mars and leading the Federation to ban synthetic life and programming for years until the Romulan plot was exposed by Jean-Luc Picard and his new crew.
When Gwyn learned what the Diviner had planned, she immediately realized that the Protostar could never go to Federation space because of the immense risk that it presents. This risk is likely how the starship was hidden on Tars Lamora, with Captain Chakotay potentially concealing it on the planet after learning what the Diviner had planned. However, this threat is still very much active and headed right for Starfleet.
To make matters all the worse, the Protostar's starship signal has been detected by Starfleet, who are similarly unaware of the danger headed their way. The Diviner may be defeated, with control of the Protostar wrested from him by his own daughter, but his final victory could still come to pass as the Protostar's new crew boldly plays right into his hands.
Created by Dan and Kevin Hageman, Star Trek: Prodigy is available to stream on Paramount+.