Warning: SPOILERS for Star Trek: Prodigy Episode 6 - "Kobayashi."
New revelations about the Diviner's (John Noble) search for the USS Protostar in Star Trek: Prodigy episode 6 appears to create a Star Trek: The Next Generation-era time travel plot hole. Newly arrived in the Gamma Quadrant, the ragtag young alien heroes led by the Hologram Janeway (Kate Mulgrew) unlock decrypted files about the USS Protostar's mission. Meanwhile, a flashback to the birth of Gwyn (Ella Purnell) poses intriguing new questions about the Diviner's quest for Starfleet's fastest ship.
The mysteries surrounding the USS Protostar are at the heart of Star Trek: Prodigy. We know that the starship was found abandoned in the Delta Quadrant mining world of Tars Lamora, which is ruled by the Diviner and his robotic enforcer, Drednok (Jimmi Simpson). The Protostar has unique capabilities; along with the training hologram of Captain Janeway, the Starfleet vessel has three warp engines, including a Proto-Drive that houses a dwarf star. Powered by the Proto-Drive, the Protostar can achieve Proto Warp and fly faster than any Starfleet ship before. After they engaged the infant star-enabled Proto Drive for the first time, even Hologram Janeway was shocked when the Protostar traveled 4,000 lightyears in minutes so that the starship left the Delta Quadrant and slowed to impulse power in the Gamma Quadrant.
However, the flashback to Stardate 43929.9, which was "17 years ago," in Star Trek: Prodigy episode 6, "Kobayashi," raises big questions about the USS Protostar's origins. 17 years ago, the Diviner was already searching for the Protostar, and he asked Drednok to sire his progeny, Gwyndala, to help him continue the Vau N'Akat race. But Star Trek: Prodigy is set in 2383 and 17 years prior is 2366, which is season 3 of Star Trek: The Next Generation. How could the Protostar already exist at that time? The starship's technology is much too advanced for that era, and it also doesn't make sense how the Protostar has a training hologram of Captain Janeway when she wasn't even a Captain yet in 2366. Kathryn Janeway didn't become the Captain of the USS Voyager until 2371.
The most obvious answer is that the USS Protostar time-traveled to 2366 from a later point in the 24th century. It's possible the Proto Drive also enables time travel, either on purpose or accidentally. This could make sense; Captain James T. Kirk (William Shatner) used the "slingshot effect" of hurtling the Starship Enterprise around the sun in order to achieve time travel in Star Trek: The Original Series and Star Trek IV: The Voyage Home. The baby star within the Proto Engine may give the Protostar the same ability to break the time barrier. This would explain the anachronisms of the Protostar's advanced technology and Hologram Janeway crashing in Tars Lamora, remaining derelict for 17 years.
But another question is how the Diviner knows about the Protostar 17 years ago if it time-traveled from the future? It's possible that the Diviner is also from the future and he was the last of the Vau N'Akat before he sired Gwyn. Yet the Diviner and Drednok curiously spoke of something called "The Order" that the Diviner seems to answer to. Another possibility that could explain the Diviner's ailing health is that he not only crossed time but universes as well. Star Trek: Discovery season 3's Temporal War revelations established that to jump across timelines from an alternate universe is lethal, and this may be what's killing the Diviner. The villain may need the Protostar to not just time travel but also cross into an alternate timeline. The Diviner's links to the Protostar could also explain why the encrypted files are in Solum, the Vau N'Akat language.
Finally, Star Trek: Prodigy episode 6 ends with the shocking reveal that Chakotay (Robert Beltran) was the original Captain of the USS Protostar and Hologram Janeway was his aide. This also opens up a slew of new questions like what caused Chakotay and his crew to abandon the Protostar? If the Protostar time traveled, were the Starfleet Officers able to flee the ship before it jumped to 2366, or have Captain Chakotay and his people been trapped in the Delta Quadrant for the last 17 years? It seems logical that the Protostar came the future but whoever controls the incredibly fast starship and its Proto Drive will be able to decide what happens next in Star Trek: Prodigy's present-day.
Star Trek: Prodigy streams Thursdays on Paramount+.