The Dominion war had more reverses of fortune than most, but perhaps the most significant of all was the capture by the Allies of a fully functional Dominion attack vessel, complete with both a new energy dampening weapon and the technical crew which had recently installed it. The Breen's unique weapons technology had put the Allies in a critical situation; only the Klingon ships had been successfully modified to resist the device, leaving them to shoulder the burden of the war alone. With the Dominion firmly back on the offensive, the Cardassian resistance movement realized that desperate action was required. Damar led a group of Cardassian freedom fighters, assisted by Colonel Kira Nerys and Elim Garak, on a daring raid against a Dominion shipyard to capture an example of the Breen weapon. Once Starfleet had its hands on the weapon and its technical crew, they were quickly able to neutralize the effects. 
By this stage it appears that the Founder commanding the Dominion's Alpha Quadrant forces had become deeply disillusioned with the conduct of the war. She decided to pull all Dominion forces back into Cardassian space, creating a defensive perimeter which she hoped the Allies would be unable to breach. Within this protected zone, the Dominion would create a vast fleet with which to launch an unstoppable offensive.
The Allies recognized the danger and launched an all-out assault on Cardassian space as soon as they were able. At the same time the Cardassian rebellion began in earnest. A popular uprising on Cardassia put most of the Dominion facilities under attack. Frustrated by the what she saw as a betrayal, the Founder ordered Weyoun to take decisive action to end the uprising. Weyouns response was to destroy Lakarian city, killing two million Cardassian civilian men, women and children. In a public broadcast he threatened to destroy another major city for each rebel attack.
The action did not have the result intended. As soon as news of the atrocity reached the battle, the Cardassian fleet turned on their Dominion allies with a vengeance. The Allies used the opportunity to launch a full attack on the Dominion fleets centre; finding themselves assaulted on all sides, the Dominion forces were destroyed or forced into retreat.
When news reached the Founder, she ordered the Jem'Hadar on Cardassia to rampage across the planet, killing as many civilians as possible. She had all available Dominion forces pulled back for a last stand at Cardassia Prime, hoping the battle would be so costly for the Allies that it would deter them from ever making an aggressive move against the Dominion again. The Allies predicted that clearing the Dominion system would cost them 40% of the combined fleet, yet they had no real alternative but to press on with the operation.
As they advanced on the system, the Cardassian rebellion mounted a desperate attack on the Founders headquarters. Weyoun had badly weakened the contingent of Jem'Hadar guarding the base in order to provide more troops for the assault on the civilian population, and the rebels were able to capture the Founder herself. Constable Odo convinced the Allies to allow him to go down to the surface of the planet and meet with the Founder. He linked with her, curing her of the disease which Section 31 had spread amongst their people and convincing her that the Federations intentions towards the Dominion remained honourable even after all it had endured. The Founder agreed to order a ceasefire and surrender herself to the Federation in return for Odos return to the Great Link to spread the cure and establish a new relationship with the 'Solids'.
The final assault on Cardassia never came; the Allies landed unopposed to find themselves on a planet devastated by the Dominion. But the cost was high; thousands of Allied Starships were lost, and over eight hundred million Cardassians perished at Jem'Hadar hands.