With the Cardassians crippled and sueing for peace against the Klingons and the Federation too busy with handling them and Dominion infiltrators, the Maquis leadership realised they actually on the verge of victory and were making bold plans to declare the creation of a new independent state under the control of neither power. Even the capture of Micheal Eddington by Captaim Sisko, the Maquis were still hopeful that their ultimate goal was just within reach. These plans would come to a tragic and bloody end however. Gul Skrain Dukat, a former officer of the Cardassian military who had gone rogue less than a year elarier would make a cataclismic decison to ally with the Dominion, with them placing him in control of the Cardassia Union and providng militarty and economic support in exchange for the Cardassians joining the Dominion, as part of their broader efforts to take control of the Alpha and Beta Quadrents. Now the head of the Cardassian goverment in with the backing of the mighty Dominion behind him, Dukat made a public address that not only would he drive out the Klingons from Cadassian space, but also that all territory that had ever been controlled by Cardassia would be returned to them, starting with the eradication of the Maquis in the DMZ within five days.
It would take only three.
The Cardassian-Dominion alliance poured across the DMZ and decimated every Maquis ship, base and world they could find. With only fighter, raiders, courier craft and freighters available to them, the Maquis did not stand a chance against the Dominion's pwerful warships and numerically superior and highly trained Jem'hadar who were ruthless and took no prisoners. Cal Hudson would be among the many to die during this onslaught. Efforts to reconsolidate or even retreat were further hampered by a Changling infiltrator who had been embedded with the organisation for several years, eventually leading to a disasterous last stand on the planet of Athos IV hidden in the Badlands where a final massacre took place. It was only thanks to the timely intervention of Captain Sisko and a newly-released Michael Eddington that anyone survived this slaughter, with only thirteen members escaping on a Sisko's runabout, some of them children, while Eddington himself would also die covering their escape.
From over 250,000 active members and thuosands more sympathisers and supporters across the DMZ and Federation and commanding 390 ships of various class or type at their height, the Maquis were reduced to only a few hundred and only half a dozen ships. While some scattered throughout space, most turned themselves over to the Federation for safety and were impriosoned, with a scant few others in Cardassian custody as well while most notably, those under the command of Chakotay were still serving onboard Voyager at this time as it was still lost in the Delta Quadrent, unaware of what had occured. Other notable survivors included Ro Laren who continued fighting and Thomas Riker who remained imprisioned with the Cardassians.
As the Dominion War finally erupted in late 2373, Starfleet would take desparate measure to turn the tide of the war in it's favour. This including providing pardons to almost all members of the Maquis in exchange for their aid in fighting the Dominion. Many would accept this offer, taking prvisional Starfleet commissions, most notably Thomas Riker, who after being freed from Cardassian imprisonment on the reccomendation of Colonel Kira, Commander Riker and the remaining members of his Maquis cell, was placed in command of the prototype USS Achillies which he used to incredible effect against Dominion fleets. Starfleet would study Maquis tactics, taking information from it's surviving members such as their tactics and knowledge of certain regions and integrate them into covert operations and gurrilla attacks where possible and potentially most effective. Thisironically proved useful when training Legate Damar's rebellion against the Dominion, which was able to score a number of critical strikes against Dominion ships and installations before the final battle of Cardassia.
In the years following the Dominion War, very little of the Maquis remained. As part of the formal end of the war, the Treaty of Bajor stipulated that the Maquis as an organisation would no longer exsist, which was ligitimised by the surviving member's of it's leadership who agreed to sign the treaty after heavy diliberations between them, the original colonists of the DMZ who remained alive and the Federation Council. However, it is arguable that the Maquis ultimate objetive was achieved. the Federation would take full control of the worlds in the former dematilariesed zone once more, with the Cardassian Union offically ceding any and all claims to them as part of the agreement for post-war aid and a permanent guarantee for protection from the Federation and Starfleet. This would help further inflame elements of the nationalistic old guard of the Cardassian government and military such as Legate Matan, Gul Kentar and the remaining members of the True Way organisation who would make several attempts to strike back against the Federation and it's allies and attempt to overthrow the new democratic Cardassian government but these ultimately failed. As of this moment, the worlds once contested by the Maquis still reside within the Federation, with the promise that they will not be abandoned again.
In relation to the current conflict with the Galactic Empire of the Skyriver Galaxy, Starfleet analysts are rexamining the Maquis's campaigns and organisation to compare them against those of the Rebel Alliance, pouring over records, material and interviewing the last few survivors of the organisation on how they conducted themselves. It is hoped that whatever can be learned from the Maquis could in turn be taught to the Alliance operative and soldiers to aid in their efforts.
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