After the Cardassians retreated from Bajor and Terok Nor, a neutral zone was created between the two organisations. There were a number of people who disagreed with the treaty and banded together. Their object was to protect their communities and that included what they referred to as resistance and others terrorism. It didn't only include low ranking personnel but also high ranking officers as well.
The first time we find out about the Maquis is in the episode The Maquis when the group is targetting Cardassian ships. The Maquis believe that the Cardassians are arming Cardassians in the neutral zone and therefore are taking out the threat by blowing up Cardassian ships. Things come to a head when Gul Dukat uncovers the truth and that the Cardassians are actually supplying their personnel in the neutral zone.
When a Maquis ship disappears in the badlands, the U.S.S. Voyager is despatched to find out what happened to it. The truth is that an alien force pulled the Maquis ship into the Delta Quadrant because he is looking for someone to take over the station that he lives on. The station looks after the well being of the Ocampan homeworld whose environment he destroyed.
When the space station is destroyed, both crews of the Maquis and Voyager agree to work together in order to get home. Chakotay who is the leader of the Maquis ship becomes Voyager's second in command.
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