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Nonetheless, various Federation members supported the Maquis ' cause, and illegally helped to supply them with weapons and other technology that they could use in their struggle.

In several cases the Federation actually intervened in the war between the Maquis and the Cardassians, aiding the latter in recognition of the peace treaty.

In one case the Federation ship tracked a Maquis vessel to the Badlands with the intention of apprehending it but an alien being sent both to the Delta Quadrant in the opposite side of the Milky Way Galaxy, where the two crews were forced to unite to survive against alien threats like the Kazon.

In following years, when the Cardassian Union joined forces with The Dominion to fight in the Dominion War against the Federation, the Dominion aided the Cardassian military in obliterating the Maquis, a prelude to their war against the Federation and its allies.