The most high-profile Starfleet traitors in Star Trek: The Next Generation and Star Trek: Deep Space Nine were united by a common goal: disapproval of the Federation's peace treaty with the Cardassians. During negotiations to end hostilities between the Cardassian Union and the Federation, various colonies were handed over to the Union, which meant that Federation-born colonists had to live under Cardassian occupation. This was a hugely controversial decision that caused unrest across the whole of the demilitarized zone (DMZ) between the Cardassian and Federation territories. This led to the formation of the Maquis - a resistance group of occupied colonists and an increasing number of disillusioned Starfleet officers.
Behind the scenes, the Maquis were originally created for Star Trek: Voyager, as a way to disrupt the standard Star Trek bridge crew. Led by Voyager's Commander Chakotay (Robert Beltran), the Maquis and Starfleet were forced to work together to find their way back to the Alpha Quadrant. In order to establish the Maquis ahead of Voyager's premiere in 1995, they were introduced through key episodes of TNG and DS9. This helped to establish the bridge dynamic of Voyager - that many of the Maquis had served in Starfleet. Among the high-profile officers who joined the resistance against the Cardassians were Will Riker's transporter clone Thomas (Jonathan Frakes) and Lieutenant Ro Laren (Michelle Forbes).
Why Ro, Riker, & Eddington Betrayed Starfleet For The Maquis
Many Starfleet officers joined the Maquis after experiencing the resistance firsthand. The first Starfleet officer to join their ranks was Calvin Hudson, a close friend of DS9's Benjamin Sisko. Hudson was assigned to the DMZ on a diplomatic mission but was horrified by what he saw, using his Starfleet connections to supply the Maquis with supplies and intel. Hudson's betrayal set the scene for Tom Riker, Ro Laren and Michael Eddington to also turn their back on Starfleet.
In TNG season 7, episode 24, "Preemptive Strike", Ro went undercover within the Maquis, only to be inspired by their fight against Cardassian oppression. This was hardly surprising given Ro's Bajoran heritage and her own disapproval of the treaty with Cardassia. Similarly, DS9's security officer Michael Eddington was also horrified by the Federation's appeasement of the Cardassians and finally switched allegiances in season 4, episode 22, "For the Cause", an episode that also revealed that Sisko's girlfriend Kassidy Yates was a Maquis smuggler.
Will Riker's transporter clone Thomas masqueraded as Will to hijack the Defiant in DS9 season 3, episode 9, "Defiant". When he was confronted by Major Kira (Nana Visitor), she claimed he only joined the Maquis to stand apart from the legendary Will Riker, Thomas refuted this and affirmed that he joined the Maquis because Starfleet refused to do anything about the oppression of colonists in the DMZ. Interestingly, Will Riker let Ro Laren escape to join the Maquis in "Preemptive Strike", which suggests he had underlying sympathies with the cause that became more overt in Thomas.
What Happened To The Maquis After DS9's Dominion War
Ultimately, the Maquis were proved right about Cardassian oppression and duplicity when Gul Dukat (Marc Alaimo) led the Union into an alliance with the Dominion. The Dominion War was disastrous for Star Trek's Maquis, Voyager season 4, episode 15, "Hunters" revealed that the resistance had been decimated by the conflict. Aside from the large Maquis contingent on Voyager, small pockets remained, while other Maquis members like Thomas Riker remained in Federation and Cardassian prisons. Eddington was killed saving Sisko, but Ro and Thomas Riker's ultimate fates are still unknown. However, the Dominion War was a devastating end to one of the most interesting, and morally complex elements of the Star Trek: The Next Generation and Star Trek: Deep Space Nine shared universe.