After Minister Jaro dismisses Major Kira and sends her back to Bajor, Sisko angrily confronts him about his actions. Jaro is surprised that Sisko is not happy to be rid of his troublesome officer, but assures him that Kira has been promoted. He also reminds Sisko that he couldn't have a better replacement than war hero Li Nalas, who will be safer from Bajor's escalating violence if he remains on Deep Space Nine. Sisko receives an eerie reminder of that violence when he returns to his quarters and finds his door has been vandalized with The Circle's insignia. Kira, meanwhile, is not happy about leaving, a fact she discusses with the rest of the crew as they stop by her quarters to see her off. Odo encourages her to fight for her job, but Kira is resigned to her fate. Then, Bajoran spiritual leader Vedek Bareil arrives unexpectedly. Although he starts out talking about the proliferation of weapons on Bajor, he ends up changing the subject and inviting Kira to spend some time at his monastery. She accepts, but before she leaves, Sisko promises to fight to have her reinstated.
In the monastery, Kira grows uncomfortable with both her feelings of uselessness and her growing attraction to Bareil. Bareil leads her to a chamber of the temple shrine, where he leaves her alone with one of the sacred orbs. Kira is suddenly enveloped by light and mysteriously transported to a room full of Bajoran legislators, plus Dax, Vedek Winn, Jaro, and Bareil. Kira is urged to listen to the legislators. Suddenly, she realizes that she is naked, just as Bareil appears from behind and kisses her. As they kiss, an explosion of sound interrupts the moment and she finds herself fully dressed, standing alone in the shrine chamber. Later, when Bareil asks Kira what she experienced, she lies about it, even when Bareil says that she has been in one of his visions.
Back on Deep Space Nine, Quark fills Odo in on an important piece of information — the Kressari have been supplying arms to The Circle. Without Kira to help him, Odo needs Quark's assistance to learn where the weapons are being delivered, and forces the Ferengi to act as his deputy. The officers delay the departure of a Kressarian freighter long enough for Odo to sneak aboard in liquid form and then disguise himself as a rat. At the same time, Sisko travels to Bajor to tell Kira about the arms shipments and warn her about the imminent coup. He again promises to help her return to the space station. However, soon after he leaves, she is drugged and kidnapped by three masked men.
On the Kressari ship, Odo learns that the Cardassians are really behind the arms shipments, secretly supplying the Kressarians with the weapons being taken to Bajor. Meanwhile, Kira awakens in an underground bunker, where Minister Jaro reveals that he is The Circle, and that he assigned Li to the station so the war hero wouldn't gain the devotion of the Bajorans. Jaro then passionately declares that, thanks to his work, Bajor will soon no longer be powerless in the face of others, and the Federation will be forced to leave. Back at the station, Quark tells Sisko where Kira has been taken, and Sisko, Li, and Bashir hurry to Bajor to rescue her. Surprising Kira's captors, they find her, cut and bleeding, and transport her back to their Runabout.
Soon after the group arrives at the station, Odo returns and informs Kira that the arms shipments to The Circle are coming from the Cardassians, who hope a resulting coup will get rid of the Federation so they can eventually retake Bajor. Back on Bajor, Jaro has no idea of this, and congratulates Vedek Winn on their pending success. Desperate, Sisko tries to put Li in touch with Bajor's Council of Ministers to tell them the truth, but all communications with the planet have been severed. Instead, he summons the aid of Admiral Chekote at Starfleet Command, and the two soon realize that Bajor is set to erupt in a full-scale revolution. With Bajoran assault ships scheduled to reach Deep Space Nine in only seven hours, the Admiral orders Sisko to conduct a complete evacuation of the station, but Sisko secretly plans to make one last stand against the approaching Bajoran forces.