Warning: SPOILERS for Star Trek: Starfleet Academy Season 1, Episode 1 – “Kids These Days” & Episode 2 – “Beta Test”Star Trek: Starfleet Academy dropped an ominous and scary hint that something tragic may have happened to Starfleet’s youngest Captain. Directed by Alex Kurtzman and written by series creator Gaia Violo, Star Trek: Starfleet Academy’s series premiere sees the USS Athena survive an attack by Nus Braka (Paul Giamatti) to arrive at San Francisco on Earth.

Before Nus Braka and the Venari Ral trapped the USS Athena to steal its warp drive, Starfleet Academy’s new class of cadets were getting oriented with each other and their professors, one of whom is The Doctor (Robert Picardo). Star Trek: Voyager‘s original Emergency Medical Hologram is now also the Chief Medical Officer of Captain Nahla Ake’s (Holly Hunter) starship.

The Doctor teaching at Starfleet Academy continues his role in Star Trek: Prodigy season 2. The EMH was one of the mentors Admiral Kathryn Janeway (Kate Mulgrew) assigned to oversee her warrant officers, the young ragtag crew of the USS Protostar, including Dal R’El (Brett Gray) and Gwyndala (Ella Purnell).

The Doctor’s Reaction To Captain Gwyndala’s Name In Star Trek: Starfleet Academy Is Scary

Naturally, Series Acclimation Mil AKA SAM (Kerrice Brooks) wanted to meet The Doctor. SAM is a Kasqian, a photonic being programmed to be a 17-year-old girl, and the EMH is Starfleet’s legendary O.G. sentient hologram. However, when The Doctor rebuffed SAM, claiming, “I’m no one’s mentor,” the Kasqian cadet name-dropped Star Trek: Prodigy’s crew to prove otherwise:

“But you were, to the Voyager crew, to the children of the Protostar, to Dal, and Murf, and Captain Gwyndala… Your sensitivity calibrations are spiking…”

Upon hearing Captain Gwyndala’s name, The Doctor spun around and glared at SAM. The EMH’s alarming spike of his “sensitivity calibrations” hints that something tragic may have happened to Gwyn, Dal, and their friends, Murf (Dee Bradley Baker), Rok-Tahk (Rylee Alazraqui), Zero (Angus Imrie), Jankom Pog (Jason Mantzoukas), and Maj’el (Michaela Dietz).

However, Star Trek: Prodigy co-executive producer and season 2’s co-head writer Aaron J. Waltke shared his thoughts on what caused The Doctor’s reaction to Captain Gwyndala’s name and more about Star Trek: Starfleet Academy‘s Prodigy callouts on Threads:

Star Trek: Prodigy season 2 ended with the teenage Gwyndala named Captain of the USS Prodigy. Their mission was to bring the light of the United Federation of Planets to unknown regions of space in the wake of the Mars Attack of 2385, which caused the Federation to cease exploration and focus on defense.

Sadly, Netflix did not order Star Trek: Prodigy season 3, so fans don’t know what became of the USS Prodigy and her crew. The Doctor’s reaction to SAM saying Captain Gwyndala’s name raises eyebrows, especially since the 800-year-old EMH remembers all events as if they had just happened.

Starfleet Academy Has A Cadet From Star Trek: Prodigy’s Brikar Species

Star Trek: Starfleet Academy‘s Star Trek: Prodigy references don’t stop at SAM shouting out Captain Gwyndala and the USS Prodigy. Star Trek: Starfleet Academy season 1, episode 2, “Beta Test,” kicks off the fall semester in San Francisco, and one of the new cadets is a Brikar.

The Brikar is the hulking, rock-like species that Rok-Tahk from Star Trek: Prodigy. Rok-Tahk was the first Brikar admitted into Starfleet Academy. While it’s unknown how many Brikars joined Starfleet in the next 800 years, Star Trek: Starfleet Academy’s new Brikar cadet continues the legacy Rok-Tahk began.

Star Trek: Starfleet Academy‘s welcome nods to Star Trek: Prodigy reaffirm the beloved animated series’ importance, especially considering how unfairly the show was treated by Paramount+. The Doctor joining Star Trek: Starfleet Academy’s cast was directly because executive producer Alex Kurtzman loved the EMH as a mentor to the cadets in Star Trek: Prodigy.

However, the ultimate fate of Captain Gwyndala and the USS Prodigy now demands a follow-up and confirmation now that Star Trek: Starfleet Academy has opened that door.