The Cardassians fought a bloody war with the Federation which finally ended in 2366 when an uneasy truce was reached. The armistice that ended the conflict was negotiated over a period of over three years by Admiral Alynna Nechayev, with Starfleet Captain Edward Jellico playing a large part in the negotiations. An item of note regarding the treaty is that Ambassador Spock openly disagreed with his father, the legendary Ambassador Sarek, over the outcome of the armistice. Border disputes would not be settled until the Federation-Cardassian Treaty in 2370.
The Federation-Cardassian Treaty established the Demilitarised zone as a buffer between the newly re-drawn Federation and Cardassian borders. Neither the Federation nor the Cardassians were allowed by the Treaty to place Military Outposts in the region, nor were they allowed to conduct fleet exercises or station warships anywhere in the DMZ. The Treaty ceded several dozen Federation colonies to the Cardassians, forcing the colonists (many of whom had been there for ten generations) to either voluntarily relocate, or forfeit their Federation Citizenship to remain in their homes under Cardassian rule.
Feeling abandoned by the Federation, a number of the colonists formed a guerrilla force to protect their homes from the Cardassians, who frequently attacked them in violation of the Treaty without any serious consequences. The guerrilla force called themselves the Maquis, after the secret army of patriots in France during the German occupation in 1940-1944. The colonists were joined by Starfleet Maquis sympathisers, former Bajoran freedom fighters, and disenchanted individuals from all walks of life who either had personal grudges against the Cardassians, or simply were looking for a fight.
The Maquis were organised in a series of cells, with only the leader of each cell knowing the whereabouts of the other cells. They hid in the Badlands, a region of space near the Cardassian border populated by dangerous Plasma Storms, much as their 20th century counterparts had hidden in the thickets from which they derived their name. The Badlands had been used by the Bajoran Resistance for the same purpose during the occupation.
The Maquis saw the Federation as willingly sacrificing their colonists in an effort to maintain a peace that should never have been negotiated. This point was brought home all too clearly when the Cardassians allied themselves with the Dominion, and declared war on the Federation and her allies in 2372. However even with the Cardassians once again as their enemy, the Federation refused to change their policies regarding the Maquis. While the Bajoran freedom fighters were lauded for driving the Cardassian occupation from their homeworld, the Maquis were condemned as terrorists and treated completely without mercy. Starfleet in particular saw the former 'Fleet personnel such as Cal Hudson, Ro Laren, Tom Riker, and Michael Eddington the Maquis as a personal betrayal.
Eventually, the Maquis were declared to have forfeited their citizenship in the Federation.
In 2373, the Maquis in the Alpha Quadrant was almost entirely wiped out by the Cardassians and Jem'Hadar, despite aid provided by the Klingons which included thirty class-4 cloaking devices. The only Maquis left alive were the crew of Chakotay's ship who had been assimilated into the Voyager crew in the Delta Quadrant, and the Maquis in Federation prisons and a handful of survivors from the late Michael Eddington's team. According to Eddington, Cal Hudson was killed in battle. The fate of Ro Laren and Tom Riker remains unknown. Tom Riker was caught and sentenced to life in a work camp on Cardassia Prime prior to the Klingon occupation of the Cardassian Homeworld.
Known members Chakotay's crew:
Of the surviving members of Chakotay's crew, there are a minimum of thirty-one Maquis who are currently surviving aboard Voyager. (This figure was arrived at my adding the 23 who have yet to be converted via mind-meld by Tuvok to the known number of brainwashed Maquis in Repression).
Episodes to watch for background and research:
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