Arguably the most ambitious arc of the franchise was envisioned to help launch Voyager, and yet it continued down fascinating roads even from that point: the creation of the Federation rebels the Maquis.
The Maquis were Federation citizens who lived on worlds affected by treaty stipulations with the Cardassians, most famous for their Occupation of Bajor, a concept introduced in The Next Generation but played out most dramatically in Deep Space Nine. Eventually it wasn’t just those directly affected, colonists living on those worlds, but Starfleet officers who renounced their commissions to stand up for what they believed in.
The first appearance of the Maquis was in the eponymous two-part episode during the second season of Deep Space Nine. In it, Sisko and an old Starfleet friend confront the problem together until Sisko realizes his friend has actually already defected.
The same basic premise plays out in “Preemptive Strike,” Next Generation, airing about little more than a week later (if you were watching at the time, it was nearly three straight weeks of Maquis intrigue across Star Trek programming, with a few weeks’ gap; if it had happened later no doubt there would have been an actual crossover, which still has yet to happen in the franchise, and probably even the debuts of some of the actual Voyager characters).
“Preemptive Strike” resonates more with fans than “The Maquis, Parts 1 & 2” thanks to pivoting around a known character rather than someone introduced in the story. That character of course is Ro Laren, the Bajoran who had been a recurring character in Next Generation for years, who was even originally considered to continue on in Deep Space Nine (and subsequently replaced by the new character Major Kira).
By the end of the episode, Ro feels conflicted by her decision to join the Maquis because she feels she’s betraying Picard directly. In that way, we end the initial experiences with the Maquis with the ability to view them in a positive manner.
When Voyager begins, “Caretaker” of course sees Starfleet and Maquis ships stranded in the Delta Quadrant and deciding to function as a single crew to find their way home again. A lot of fans expected the series to be an endless sequence of the competing ideologies in conflict, and never really forgave it for making a different creative choice. Though, to be fair, the Maquis were former Federation and in most cases even former Starfleet; the biggest hurdle was reintegrating into rigid Starfleet procedures (played out in the episode “Learning Curve”).
The Maquis story instead picks back up in Deep Space Nine, third season, “Defiant,” in which Riker’s transporter duplicate Thomas (“Second Chances”) is the third major defector we see play out, although the fourth and final one, in the fourth season’s “For the Cause,” ends up being by far the most dramatic one.
At first Sisko believes it’s his girlfriend Kasidy Yates, which would certainly be bad enough, but it turns out to be straight arrow security officer Michael Eddington, a reliable recurring presence since the previous season.
We find out how powerfully Sisko feels this betrayal in the fifth season. “For the Uniform” is arguably the pinnacle of the pre-Dominion War period for the series. Sisko swears to bring Eddington in, but this proves incredibly difficult.
However, once accomplished it becomes a definitive turning point for the Maquis. When the Cardassians join the Dominion, they enact a scorched earth policy against the Maquis, and Eddington finds himself imagining a heroic last stand in “Blaze of Glory.”
The fate of the Maquis is transmitted to Janeway’s crew in Voyager, and in “Extreme Risk” we see how powerfully it affects B’Elanna Torres, the hotheaded half Klingon, half human engineer.
Finally, in “Repression,” a sleeper suggestion is awakened among the former Maquis members of the crew, implanted by a zealous Bajoran years earlier, thereby somewhat bringing the whole arc full circle.
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