Some time later, Bajoran raiders, led by Colonel Day and Over-General Krim, arrive at Deep Space Nine. Seeing no Federation members anywhere, they cautiously assume that the station has been abandoned, not realizing that a small team led by Sisko is hiding. Eventually, however, Krim decides that some people may still be aboard when it's noticed that the internal security system has been disabled. He reports this to Minister Jaro, who reminds Krim and Day that it is most important they take Li Nalas alive, to seal their victory.

Hidden in the conduits, Sisko and Bashir command two teams of would-be resisters, while Odo spies on the Bajorans. When Odo reports that a six-man team is preparing to search the cargo deck, Bashir and his group successfully intercept the soldiers and take them prisoner. Meanwhile, on one of Bajor's moons, Kira and Dax locate a dilapidated raider and manage to get it flying, but are soon intercepted by two highly superior Bajoran ships. Kira attempts to fly into Bajor's atmosphere to evade the attacking vessels, but they are hit and crash onto the planet's surface.

In an effort to stall the Bajorans, Day is lured into a holosuite, where he attempts to "capture" holographic images of the crew. The images fade from view and the door locks, giving Sisko, via voice communication, an opportunity to tell Day about the Cardassian plot, and that proof is on the way to Bajor. However, Day is unimpressed and neglects to tell Krim about the plot after he is released from the suite. Instead, they set about searching the conduits for the Starfleet team.

Amidst the Runabout wreckage, Kira, who is badly hurt, tries to convince Dax to leave her and deliver the evidence to the Chamber of Ministers herself. But Dax refuses to abandon Kira, and the two are soon discovered. Luckily, the Bajorans who found them have been sent by Bareil, who has Kira's wounds tended to at his monastery and helps disguise her and Dax as monks. Despite Kira's protests, he insists on accompanying the women to the Chamber of Ministers. Back at the station, Bashir creates a diversion, giving an armed O'Brien, Li, and Sisko access to Krim, who they eventually corner at gunpoint, forcing him to listen.

On Bajor, a session of the Chamber of Ministers is interrupted by the arrival of Kira, Dax, and Bareil. Jaro immediately recognizes Kira and orders guards to seize her, but she tells the Ministers about how the Cardassians are secretly behind the coup and provides evidence to prove it. Jaro is left in a state of shock, refusing to believe that he has played into the hands of the Cardassians. Vedek Winn quickly sides with Kira and the other Ministers against her one-time ally. The news soon reaches Deep Space Nine, where Krim, realizing that Bajor's provisional government still stands, recognizes that it is his duty to return the station to Sisko and the Federation, and does so. However, Day refuses to give up the fight, and pulls a phaser on Sisko. Li steps in to take the full force of the shot and dies, escaping the responsibility of leadership that he dreaded so much. The next day, the crew, especially Kira, mourns Li's loss, but their sadness is tempered by the arrival of the evacuees and the realization that life on Deep Space Nine will soon be back to normal.