At the end of its war with the Cardassian Union, the Federation agreed to a new border, with some territory that belonged to the Federation before the war transferred to the Cardassians. A few Federation citizens living in colonies in the ceded territory refused to leave, and the Federation allowed them to stay, notifying them that by doing so they surrendered their Federation citizenship and would receive no support in the event of Cardassian oppression.
Cardassian oppression soon followed, and true to its word, the Federation refused to assist its former citizens. The isolated colonists managed to acquire their own weapons and space ships, however, with which they fought a guerilla campaign against the Cardassians. Surprisingly, the Cardassians asked the Federation to help suppress the Maquis attacks, and -- even more surprisingly -- the Federation agreed, leaving the Maquis fighting a two-front guerilla war against both the Cardassians and the Federation.
Because of the nature of the area causing sensor disruptions and limiting actions by starships not configured to operating there, the Maquis used the area of space known as The Badlands as a base of operation or point of retreat to escape retaliation. The ship commanded by Chakotay was running from a Cardassian Warship when it disappeared in this location. Investigating the disappearance lead to the Federation Starship USS Voyager following it into The Badlands to also disappear as well.
The Maquis and all of the former Federation colonists were eventually wiped out by the Jem'Hadar after the Cardassian Union, reeling from attacks by the Klingon Empire, decided to ally itself with the Dominion.
With no shipyards of their own and limited resources for acquiring military equipment, the Maquis were little more than a nuisance to the Cardassian Union. They can only be considered a minor power by Star Trek standards.