In his quarters, Julian Bashir and Ezri Dax wake up having slept together for the first time the night before. The two are enjoying their new relationship, however Julian worries that now that they're together something might happen to them... for the two are due to set off that day for the long-awaited invasion of Cardassia. Ezri makes a pact for the two of them... they're both coming back alive.
Miles and Keiko O'Brien continue to raise their two children, Molly and Kirayoshi. They are a family excited to be returning to Earth after the end of the Dominion War so Miles can teach at Starfleet Academy; Miles just hasn't yet found the time to inform his best buddy, Julian, nor has he had the time to give him the model of the battle of the Alamo. Miles promises Keiko he'll tell Julian about his departure when he thinks he's ready to hear it but it's clear he's not looking forward to breaking the news.
In the Sisko quarters, Benjamin comforts a pregnant Kasidy, who is experiencing morning sickness. Jake drops by to walk his father to the new Defiant on what everyone hopes to be the final mission of the war.
Odo and Worf walk to the Defiant. They both hope to find Kira alive and well when they reach Cardassia Prime; Kira, meanwhile, is still hiding in Mila's basement with Damar and Garak, planning the Cardassian Rebellion.
On the bridge of the Defiant (formerly the USS São Paulo), while talking to Odo, Sisko has another vision from the prophet appearing as Sarah, his mother. She tells the Emissary that his task is nearing completion, and that, cryptically, his journey's end lies not before him, but behind him.
At Dominion headquarters on Cardassia, Weyoun notes the Alliance's advance on their territory, and will pass the border in the morning. The Female Changeling is then talking with Thot Pran of the Breen, promising both Romulus and Earth as reward if they win the war. While Pran takes his leave, Weyoun asks the Founder why she was promising the Breen when she firmly stated he would have control of all Federation territories, including Earth, which he had been promised. She responds that she would promise the Breen the entire Alpha Quadrant to win the war at any cost. Just then, Legate Broca reports that Damar is still alive, and he is in the capital city. Yet he won't be for long.
Damar and Garak are stopped on the streets of the Cardassian capital by two Jem'Hadar soldiers, recognizing Damar, who Garak claims that he is his cousin. The Jem'Hadar silence him, telling them Damar will be taken in for questioning, while Garak will be killed on the spot. Suddenly, a Breen comes, who the Jem'Hadar can't understand and who kills them on the spot. It was actually Kira, disguised as the Breen; they safely continue on their way to the resistance meeting, where they plan the following day's course of action: sabotaging Cardassian power plants and communication headquarters, thereby cutting off the Dominion fleet from communication with headquarters.
On Bajor, Dukat enters the quarters of Kai Winn Adami, having regained his vision from the forgiving Pah-wraiths. The Kai has learned the secrets of the Book of the Kosst Amojan, and claims to have been waiting for Dukat. Together, they embark to the depths of the Fire Caves to release the Pah-wraiths, who they hope will gain control of the Celestial Temple and destroy the Prophets... and their Emissary, Winn adds. But Dukat announces that Sisko's fate will be left to him, however Winn points out that he may not survive the invasion of Cardassia. Dukat isn't worried, he's certain that Sisko will survive... and looks forward to dealing with him afterwards.
Quark, meanwhile, is passing time by playing "Go Fish" with Vic Fontaine in the holosuite wishing he was playing Tongo instead, but unfortunately, the game is not programmed into Vic. Quark's is experiencing a noticeable lull in business, in light of the heightened war effort and Quark can't help but worry about Nog and the others and complains to Vic that people pass through his bar looking for a good time, never bothering to notice that he doesn't have a good time as he's too busy making sure everyone else does. Vic tells Quark that the life of a bartender is a lonely one. But, alas, even Vic has better plans than Quark – he departs with a beautiful date to see Jimmy Durante and Peter Lawford at the Sands. Quark reminds Vic that a bartender's life is a lonely one, but Vic reminds Quark that he isn't a bartender.
As the Female Changeling orders the Breen to fight side-by-side with the Jem'Hadar, suddenly all power is lost on the station. As emergency power comes on, Broca announces that the power disruption was due to an act of sabotage by civilians. The Founder grabs him by the throat, suspending him in mid-air, furious that the general population is rebelling. Broca, gasping for air, assures her it is an isolated uprising, and agrees that the civilians be punished for acts of resistance. Their long-range communications (and ability to communicate with their fleet) are still not working. When power is restored to the Capitol, about half an hour later, Weyoun appears in a general broadcast message, announcing the complete destruction of Lakarian City in retaliation for Cardassian acts of sabotage; Lakarian City was home to two million souls.
Klingon Chancellor Martok hails Captain Sisko and Admiral Ross, promising to drink a celebratory barrel of 2309 bloodwine with them on Cardassia Prime. Sisko, along with the entire Starfleet attack force, engages the Dominion Jem'Hadar fighters and Breen vessels in the Cardassian system. (The Dominion has been backed up to the Cardassian system in the Alpha Quadrant at this late stage of the war.) As the dogfights ensue, several Jem'Hadar fighters appear to ram Klingon Bird-of-Prey ships in apparent suicide runs.
The Defiant (with her new name already stenciled onto her hull) is in the thick of the battle, charging into enemy lines. Miles suffers a shoulder wound from exploding bridge debris and, during the heat of the battle, finally gets up the nerve to tell Julian that he and Keiko will be leaving Deep Space 9 for Earth; Miles has accepted a position teaching engineering at Starfleet Academy. Ross orders Sisko to take the Defiant to help bolster the Romulan line; the Romulans have just lost their flagship.
Back on Cardassia Prime, Dominion headquarters still cannot communicate with their fleet; they have no idea how the battle is going for either side. At Mila's house, a squad of Jem'Hadar and Cardassian soldiers knocks on her door as Kira, Garak and Damar hide in the basement. Suddenly, Mila's corpse is dumped down the stairs to the basement, and the Jem'Hadar also throw down a stun grenade, easily subduing the trio. The Female Changeling orders Damar's immediate execution, but some of Damar's loyal Cardassian soldiers shoot the Jem'Hadar before they can execute them.
In the midst of battle, the Cardassian fleet suddenly switches sides, and begins attacking the Breen and Jem'Hadar. When communications are brought back online, the Female Changeling, shocked of the Cardassian betrayal, orders the extermination of the entire Cardassian population. Legate Broca is escorted out the door by Jem'Hadar for execution. As the Cardassian Capitol is being reduced to rubble building by building, the resistance moves into action. Garak mourns for Mila, a part of his life since he was a child growing up. When Kira tells Garak he can fight for a new Cardassia, he decides his new motivation for destroying the Dominion is revenge.
Damar's resistance reaches Dominion Headquarters, and find the entrance protected by a neutronium door. Damar suggests pretending to give himself up, but Kira warns him he'll be shot on sight. But the door opens from within, as a pair of Jem'Hadar execute Legate Broca and two other Cardassians with bayonets and dispose of their bodies. The Cardassians kill the Jem'Hadar, and engages in a fire fight with several other Jem'Hadar. While the resistance succeeds in breaking into the compound, Damar is fatally wounded and dies in Garak's lap.
Back on Bajor, Dukat and the Kai have reached their final destination in the fire caves. As the Kai begins reading from the sacred text of the Kosst Amojan, the vast underground cavern springs to life, engulfed with billows of red flame. She discards her Kai vestment, throwing it into the raging fire pit before them. She continues reading from the sacred text, invoking the spirit of the Pah-wraiths.
The Federation Alliance has cornered the Dominion all the way back to Cardassia Prime and prepares to move in for the kill. Admiral Ross proposes a three-pronged attack: the Romulans and Cardassians will attack the Jem'Hadar; Chancellor Martok will lead the Klingons against the Breen; and the Federation will knock out the orbital weapon platforms. Aboard the Defiant, Captain Sisko expects a difficult fight ahead.
The Cardassian rebellion breaks through into the heart of Dominion headquarters, capturing Weyoun and the Female Changeling. Weyoun asks where Damar was. Kira answered that he died for Cardassia. Garak shoots and kills the last-ever Weyoun clone for insulting Damar and gloating about the terrible destruction of Cardassia. Kira tells the Founder that the Dominion has lost the war, but the Founder refuses to surrender, promising a fight to the bitter end. With the Breen and Jem'Hadar fighting to the last man, the Alpha Quadrant would never threaten the Gamma Quadrant.
In the fire caves, Winn pours a toast, offering it to Dukat (still appearing as a Bajoran). He drinks from the cup; however, he soon bends over in pain. The ex-Kai admits to poisoning him, as a sacrifice for the Pah-wraiths, who better than Dukat? Dukat sprawls and dies. She then proceed to awaken the Wraiths.