The fifth episode of Star Trek: Starfleet Academy focuses on the holographic cadet SAM, played by Kerrice Brooks. SAM is short for “Series Acclimation MIL,” which is also the name of the episode. But the episode is also a love letter to Deep Space Nine, the way-ahead-of-its-time 1990s Trek series that has become a fan-favorite. The episode also features two characters from that show making a welcome return. And it grapples with a long-standing mystery that the series left behind when it ended in 1999. It is about the fate of DS9’s lead character, Captain Benjamin Sisko (Avery Brooks).
SAM Tries to Unravel the Mystery of Deep Space Nine’s Missing Captain Sisko

SAM is an emissary for her photonic (holographic) species, the Kasqians, who sent her to the Academy to learn about organic beings. Thousands of years ago, the Kasqians were created by organics, then used as slaves until finally abandoned. In an attempt to understand organics better, they created SAM mere months before the series began, programming her with the mind and attitude of a 17-year-old human.
As an emissary herself, SAM decides to unravel the mystery of another famous emissary, Captain Benjamin Sisko, commander of station Deep Space Nine and Emissary of the Prophets of Bajor. To do so, she enlists in the Academy’s seminar, “Confronting the Unexplainable.” One of the unexplained mysteries they teach is what became of Ben Sisko after the events of the Deep Space Nine finale, “What You Leave Behind.”
The Complex Life (and Death?) of Deep Space Nine’s Captain Benjamin Sisko

In Deep Space Nine, the space station was adjacent to the planet Bajor and technically their property. Starfleet sent Commander Benjamin Sisko to operate the station after Bajor freed itself from Cardassian occupation. The Bajoran religion taught that there was a Celestial Temple in the heavens, a home to powerful Prophets who guided them and whom they worshipped as gods. When Sisko took over DS9, he discovered a stable wormhole near the planet. This was home to non-corporeal beings who exist outside of time. They are the same entities that the Bajorans worship as gods. The Bajorans determined the wormhole was itself the Celestial Temple. Therefore, Benjamin Sisko was the Emissary of the Prophets who had long been foretold to them.

Sisko struggled with his role as Starfleet officer and religious figure over the seven seasons of DS9. Slowly, he embraced his religious role. Towards the end of DS9, he discovered his mother Sarah was a part-human, part-Prophet, and these beings actually engineered his birth. After saving Starfleet from the Dominion, he went into the Fire Caves of Bajor to confront the malevolent entities known as the Pah Wraiths. Although he defeated them, he seemingly died in the battle.
However, he appeared to his wife, Kasidy Yates-Sisko. He told her that he now existed as a non-corporeal being within the Celestial Temple. To the Bajorans, he had fully transcended into a messianic figure. He promised his pregnant wife he would return one day. But 800 years later, in the 32nd century, it seems he never did. What really became of Ben Sisko became a galactic mystery.
SAM Takes Starfleet Academy’s “Confronting the Unexplainable” Course to Solve the Sisko Mystery

Even though it’s late in the semester, SAM talks to the instructor of “Confronting the Unexplainable,” Professor Illa, a Cardassian played by series writer (and Lower Decks star) Tawny Newsome. Among the courses are ones on the Guardian of Forever from TOS and “Alternate Continuums” about parallel timelines like the Mirror Universe. There’s also a course on how the Galactic Barrier alters mental powers, a reference to the TOS episode “Where No Man Has Gone Before.” But it’s the mystery of Captain Sisko and what truly became of him that SAM wants to solve. She believes that if she can do this, she can prove herself to her photonic makers.
Two Main Deep Space Nine Characters Return in Starfleet Academy

Thanks to Captain Ake’s advice, SAM visits the Ben Sisko Museum. There, she learns about his New Orleans childhood, his love of baseball, and his Starfleet accomplishments. She even watches a hologram of his adult son Jake talking about the great man his father was. DS9 actor Cirroc Lofton reprises the role after 25 years. But she’s still no closer to discovering the truth. Starfleet agents never found his body, so they declared him MIA. But to the Bajorans, a central tenet of their religion is that the Emissary lives forever in the Celestial Temple, watching over them. But it’s all faith. They have no concrete proof.
Eventually, SAM has to admit to Professor Illa that she failed at solving the mystery. The Professor tells SAM that Benjamin’s son Jake was an author. And he wrote a book about his father titled Anslem but he never published it. But she just so happens to have the only copy. Maybe it contains the answers SAM needs. When SAM reads it, she feels the presence of Jake Sisko talking to her. He explains that to him, his father never actually left, and he was always there with them throughout their lives.

SAM also learns that Professor Illa is half Cardassian/half Trill and is actually Illa Dax, the current host of the Dax symbiote. That means she knew Ben Sisko personally and was his mentor and friend hundreds of years ago. That’s why Jake entrusted her with his book.
Does Starfleet Academy Solve the Riddle of Captain Sisko?
Does this episode solve the mystery of the missing Captain Sisko? Well, for Star Trek fans, what became of Sisko was never a mystery. We know he went to exist with the Prophets in the Celestial Temple/wormhole. However, actor Avery Brooks insisted they include a line in the DS9 finale, where Sisko appears to his pregnant wife, Kasidy. He promises he will return to her and their unborn child. Brooks insisted they add that into the script. He believed the optics of a Black man abandoning his wife and child were destructive stereotypes. The question isn’t “What happened to Sisko?” It’s “Did Sisko ever return?” And judging from this Starfleet Academy episode, it seems he did not, which is a bummer. Or, is Jake actually telling us that he did?

Jake, at least Sam’s idea of Jake, insists that his father never really left his family. He was always present in their lives, he said. But was Jake Sisko being figurative or being literal? As a non-corporeal being, or Prophet, he could possess organic humanoids if he wanted. This happened on occasion on DS9. It’s possible Ben Sisko did this, and was able to be with his wife and kids. And all without the galaxy at large ever knowing about it. But if that’s what happened, Jake Sisko certainly never told anyone. It’s a secret he took to his grave. This episode only gave us the vaguest hint of that possibility.
The Door Is Open for Avery Brooks to Return as The Emissary in Star Trek

Avery Brooks is a very reclusive figure, whose last screen credit is 2001’s 15 Minutes. He’s continued to narrate documentaries and appear on stage. Tawny Newsome, a writer on Starfleet Academy and former Lower Decks cast member, is a huge Deep Space Nine fangirl. And she even co-wrote this chapter. She also got approval to use Avery Brooks’ spoken word reading to close out the episode. So we do hear Sisko’s voice, and the episode is dedicated to him. But it seems Brooks probably declined to appear on screen. But if Brooks wants to ever return and truly resolve this mystery, we know Trek fans would love to see it.
Star Trek: Starfleet Academy is currently streaming on Paramount+.