As the Bajoran assault vessels approach Deep Space Nine, Sisko announces that he is evacuating the station's civilian population and anyone who wishes to leave. The entire crew volunteers to stay with him and fight, and various people react differently: Jake Sisko and Nog find out they will be on different runabouts but determine to stay friends, Keiko O'Brien urges her husband, Miles to leave with her, and Quark decides to broker nonexistent additional seats. Li Nalas calms the resulting flood of passengers by inspiring courage in his fellow Bajorans; Quark is subsequently left on the station when his brother Rom outdoes him in deviousness and sells Quark's seat to a Dabo girl.
Once the Bajoran forces arrive, there is no sign of Federation presence but General Krim is highly suspicious. The station's security net is disabled and the Federation crew is unaccounted for, leading him to believe they are still aboard. Jaro orders Krim to capture Li Nalas alive, convinced that he can bribe Li into joining the Circle. When the sensor array is sabotaged, his suspicions are confirmed and the soldiers begin a search of the station. Odo uses his shapeshifting abilities to help the crew avoid detection and capture a number of soldiers during the search.
One of the runabouts drops Kira and Dax off on a Bajoran moon where the Bajorans stored a number of small starfighters during the Cardassian occupation. They manage to get one of the craft working and Dax is disoriented by the lack of technology, to which Kira tells her they are flying "by the seat of (our) pants". Bajoran fighters intercept them and a dogfight ensues. Their ship is shot down during the fight and they crash.
Sisko and the crew successfully keep the Bajoran soldiers at bay until a group led by Krim's second-in-command, Colonel Day, discovers Sisko, Li and O'Brien in one of Quark's holosuites. However, it is a trap and Sisko informs the soldiers about the Cardassian involvement in the Circle. He releases Day to pass the information to Krim, but the colonel instead tells Krim that the Federation is attempting to wrest control of DS9 from the Bajorans. A scan for Federation communicator signals reveals they are somewhere in the conduits and Odo informs Sisko that the soldiers intend to flood the conduits with lethal neurosine gas. Part of the crew distracts the bulk of the Bajoran forces, after which Li and Sisko capture Krim in an attempt to reason with him.
Although Kira was injured in the crash, Dax gets her to Vedek Bareil's monastery. She and Kira disguise themselves as vedeks to allow them to travel to the Chamber of Ministers. Once there, Jaro attempts to dismiss Kira as a troublemaker. However, she confronts him about the Cardassian involvement, specifically, that they have been supplying the Circle with weapons. Upon hearing this information, Vedek Winn insists on examining the new evidence. Jaro announces that he will cooperate with any investigation.
Upon learning of the Cardassian involvement, Krim gives control of DS9 back to Sisko. However, Colonel Day attempts to assassinate Sisko in revenge; Li Nalas steps in the way of Day's weapon blast and is killed. O'Brien is confused by the way the Bajorans herald Li Nalas as someone who he was not. Sisko tells him Li was a hero of the resistance and that is the way he will remember him.