Star Trek: Deep Space Nine’s Biggest Unanswered Questions

In Season 3’s “Defiant,” Jonathan Frakes guest stars as Thomas Riker, the transporter double of Will Riker we meet in the Star Trek: The Next Generation episode “Second Chances.” Thomas, now a member of the Maquis, takes over the Defiant and uses it to cause trouble in Cardassian space, including exposing a hidden fleet of cloaked Cardassian ships.

Thomas willingly turns himself over to Cardassian authorities and in exchange he’s granted a life sentence of labor rather than death. Before he transports off the Defiant, Kira (Nana Visitor) promises to find a way to free him, but we never hear from him again.

Perhaps the most likely possibility is that Thomas — along with the rest of the Maquis being held by the Cardassians — was executed after the Dominion took over the Cardassian Empire. However, you would think both Cardassian and Dominion authorities would recognize the unique opportunities presented by a man who is a precise copy of a high ranking Starfleet officer.

In “Captive Pursuit,” Star Trek: Deep Space Nine‘s fifth episode, the titular station receives its first visitor from the Gamma Quadrant (at least, in terms of aliens who knew that’s where they were from) in the form of the reptilian Tosk (Scott McDonald). We eventually learn Tosk is the prey in some kind of ritual hunt. Tosk doesn’t see the hunt as a bad thing, but as the conclusion to what he’s prepared for his entire life.

Chief O’Brien (Colm Meaney) helps Tosk escape DS9 and his hunters are killed in the process. But it’s made clear more hunters will come for Tosk.

While it seems like Tosk fully expects to eventually be killed by the hunters, the unique situation of Star Trek: Deep Space Nine makes that less certain.

Anyone looking to pursue Tosk would need to come through the Bajoran Wormhole, meaning the folks on DS9 would detect them, and the officers at the station would no doubt recognize the same ships that had come looking for Tosk in “Captive Pursuit.”

That doesn’t mean the Star Trek heroes would necessarily attempt to stop those ships, but for those ships to come through the wormhole, track down Tosk in the Alpha Quadrant and kill him, and then return home (necessitating once again exposing themselves to DS9 to go back through the wormhole) with us not hearing about it seems like a pretty huge omission.

Long before Star Trek: Discovery based a huge chunk of its first season off of it, DS9 was the first show since the original series to bring fans back to the Mirror Universe starting with Season 2’s “Crossover.” We learned that since The Original Series‘ “Mirror, Mirror,” the Terran Empire had fallen to the Klingon-Cardassian Alliance. Most Terrans lived as slaves.

Over the course of DS9, the show occasionally turned back to the dark reflection, revealing more twisted versions of prime universe heroes as well as telling the ongoing tale of the Terran rebellion against the KCA.

By Star Trek: Deep Space Nine‘s final visit through the mirror, in Season 7’s “The Emperor’s New Cloak,” things are looking good for the Terrans and their allies, but the war is far from over. There’s also the nagging suspicion that if the Terrans do succeed, they’ll go back to their brutal way of life chronicled in “Mirror, Mirror.”

But however things turned out, you won’t find the answer in any of the Trek movies or shows streaming on Paramount+.

Introduced in the Star Trek: Deep Space Nine series premiere, Kai Opaka (Camille Saviola) suffers a strange fate. She dies and is reborn, but she can only continue to live if she remains on a war-torn planet.

In Season 1’s “Battle Lines,” Opaka accompanies Sisko, Kira, and Dr. Bashir (Alexander Siddig) on a trip to the Gamma Quadrant. The four of them crash on a planet whose only living residents have been there for a long time. Locked in constant, violent conflict, they are placed on the planet along with nanite technology that resurrects them over and over again no matter how many times they kill each other.

Opaka dies when the Starfleet runabout crashes on the planet and is resurrected by the nanites. She chooses to stay on the planet and minister to the people imprisoned there, deciding this is the will of the Prophets.

While Opaka does appear in later episodes of Star Trek: Deep Space Nine — in prophetic visions and dreams — we never learn if Opaka and the prisoners of the planet escape their imposed immortality.

The fan-favorite episode “In the Pale Moonlight” tells us of how Ben Sisko conspires with Garak (Anthony Robinson) to trick the Romulans into joining the Dominion War on the side of the Federation and the Klingon Empire. Their plan succeeds, but only because Garak murders a number of people, chief among them a Romulan senator.

We never learn if the Romulans discover the conspiracy that tricked them into the war, and not long after the events of DS9, the empire suffers another one of its many coups in 2002’s Star Trek: Nemesis. So if any of the Romulans had learned of Sisko’s conspiracy, that information may have been lost in Shinzon’s (Tom Hardy) takeover.

Another possibility is that certain elements of the Romulan government knew about the conspiracy the entire time and were more than happy to play along. The Romulan Tal Shiar, after all, was decimated in Season 3 after joining the Cardassians in a failed first strike against the Dominion.

If, hypothetically speaking, during or shortly after the events of “In the Pale Moonlight” what remained of the Tal Shiar learned what Sisko and Garak were up to, they might have wanted them to succeed.

In Star Trek: Deep Space Nine‘s final season, in the episode “Chimera,” we’re introduced to the Changeling Laas (J.G. Hertzler). Like Odo (Rene Auberjonois), Laas is one of the hundred Changelings who were cast out of the Great Link as infants in the hopes of gathering intelligence on the rest of the galaxy. Before leaving DS9, Laas tries and fails to convince Odo to come with him to search for the rest of the hundred.

We never learn of whether or not Laas succeeds in finding any of the other hundred, and because of what unfolds in the rest of the final season, we tend to hope he failed.

Before Star Trek: Deep Space Nine ends, we learn Section 31 arranged to have Odo infected with a virus that eventually begins killing him, the Female Changeling (Salome Jens) stuck in the Alpha Quadrant, and all the Changelings in the Great Link. Because Laas and Odo linked during “Chimera,” Laas must have also been infected, but presumably would never have had access to the cure that saves Odo and the others.

The final season of Star Trek: Picard reveals Changelings who were experimented upon by Starfleet during the Dominion War, but it’s said these were Changelings who had at one point been a part of the Great Link and so would not have been part of the hundred.

The holographic character Vic Fontaine (James Darren) is something of a polarizing figure in Star Trek: Deep Space Nine. You either love him or hate him. One thing fans in the “hate him” camp would happily point out is that it’s never really explained what makes Vic tick.

Vic is a self-aware hologram. He knows he’s a hologram and can actually turn himself on and off at will.

That makes him even more advanced than Star Trek: Voyager‘s The Doctor (Robert Picardo). Like Vic, The Doctor knows he’s a hologram, but he’s only able to turn himself on and off after the crew grants him those permissions.

But we never get any indication about why or how Vic is so advanced.

The final Mirror Universe episode, “The Emperor’s New Cloak,” adds more mystery to his story. It turns out there’s a Mirror Universe version of Vic, but he’s a flesh and blood Terran instead of a hologram.

After The Prophets call him to their “Temple” in the Star Trek: Deep Space Nine finale, Sisko promises Kasidy (Penny Johnson Jerald) that he’ll eventually return. But we’re all still waiting.

He has returned in IDW’s current Star Trek comic to stop the murderous crusade of the Klingon Emperor Kahless II, but when it comes to Trek nothing outside the television series and films have been considered strictly canonical.

In fact, we would seem to have already been shown — not once but twice — that IDW’s Star Trek isn’t canon.

First, because the screen franchise did return, however briefly, to DS9 in the Season 3 Star Trek: Lower Decks episode “Hear All, Trust Nothing” with Sisko nowhere in sight. Since the comic takes place before the events of Star Trek: Nemesis, that would put it a few years before the Lower Decks episode.

Second, because at the very end of IDW’s Star Trek #1, we see Kahless wipe out the last of the galaxy’s crystalline entities. Yet we see many of those same entities show up in Season 3 of Star Trek: Picard, which is set decades after the comic.