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The trouble is Earth. On Earth there is no poverty, no crime, no war. You look out the window of Starfleet Headquarters and you see paradise. It's easy to be a saint in paradise, but the Maquis do not live in paradise. Out there in the demilitarized zone all the problems haven't been solved yet. Out there, there are no saints, just people - angry, scared, determined people who are going to do whatever it takes to survive, whether it meets with Federation approval or not. - Benjamin Sisco, The Maquis, Part II

The Maquis are a group of freedom fighters made up of both humans and other races, such as Bajorans, who refused to give up the planets they had colonised after they were ceded to the Cardassians as part of the treaty that ended the war between the United Federation of Planets and the Cardassian Union. Later many others joined them out of sympathy for their cause, including a number of Starfleet officers who resigned their posts to join.

The Maquis viewed themselves as a resistance movement, but were regarded by both the Federation and the Cardassians as terrorists, having committed numerous transgressions against both the Cardassians and Starfleet (including theft, sabotage, and attacks on their ships) though they usually avoided attacking Federation ships directly, instead warning them to get out of the way.

In Star Trek: Freedom's timeline the Maquis demanded and received official recognition as a separate entity resulting in a peace accord being signed in 2388, and in 2404 a Maquis fleet assisted the Starfleet forces against a rebel Cardassian force led by Gul Dulon in the Battle for Bajor.

Relations between the Federation and the Maquis remain strained. Old memories on both sides die hard.

In the canon timeline the Maquis were eventually wiped out almost entirely by the Dominion. Exceptions were the Maquis who had joined the crew of the USS Voyager, and a few captured members of the movement in Federation prisons. Deep Space Nine commander Captain Benjamin Sisko believed there may have been a few other survivors who were biding their time, waiting for the right moment to strike.