Three months after the events of "Call to Arms", the Federation-Klingon alliance is badly losing the Dominion War. After hearing news that the Seventh Fleet was almost obliterated, Captain Benjamin Sisko and his command crew are assigned to pilot a captured Jem'Hadar attack ship into Dominion/Cardassian territory and destroy a valuable stockpile of Ketracel White. This would kill many of the Dominion's Jem'Hadar foot soldiers. The Federation hopes that this strike would stem the tide of the war.
The crew encounter several setbacks. First, the navigational eyepieces used on the Jem'Hadar vessel induce headaches among humans who use them, including Captain Sisko. Elim Garak notes that Gul Dukat was previously seen using such an eyepiece without apparent ill effects, and so volunteers to wear the eyepiece and be the crew's "eyes and ears" in space.
In a second incident, Sisko's ship is fired upon by the USS Centaur, which is unaware that Sisko's ship is staffed by fellow Federation officers. Both ships escape but the danger is not over yet: the Starfleet officers are now deep behind enemy lines. They accomplish their mission but the ship's warp engines are heavily damaged. It will take them seventeen years to get back to Federation territory at the speeds they can manage... if they even survive.
Meanwhile, on Terok Nor, Kira, Odo, Quark, and Jake adjust to living under the Dominion but suffer hardships. Jake stayed to write about the occupation for the Federation News Service, but Weyoun is withholding all of his articles (claiming they are biased against the Dominion), and will only broadcast his articles if he sees there is "open-mindedness" of the Dominion. Odo no longer has his Bajoran security deputies. Kira recalls memories of living under the Cardassians. Quark, however, is making the most of it and states that this occupation is not nearly as bad as the Cardassians. Dukat boasts how well the war is going for the Dominion-Cardassian Alliance, though he has failed in his attempts to dismantle the minefield. Friction begins forming between Dukat and Weyoun; Dukat is egotistically optimistic that they will conquer the Federation while Weyoun knows they are vulnerable without reinforcement and resupply from the Gamma Quadrant.
Kira convinces Odo to use his status as a Founder to get what he wants. Genetically programmed to see him as a god, Weyoun instantly accepts Odo's request to reinstate his deputies. He is also offered a seat on the station's Ruling Council, giving him a voice in station policy. He accepts.