Starfleet Command orders Captain Benjamin Sisko to prevent further Dominion reinforcements from reaching Cardassia, their first foothold in the Alpha Quadrant. A plan is devised to block the entrance to the wormhole with a field of self-replicating mines, but the mines cannot be activated until they are entirely deployed; this task will take several hours to complete. Shortly after deployment begins, Weyoun declares that Deep Space Nine will be attacked unless the mines are removed.
Knowing that Starfleet reinforcements are unavailable, Sisko asks General Martok to patrol the border while the Defiant continues deployment. Sisko also notifies Kira that he will endorse the non-aggression pact offered to Bajor by the Dominion, in the hope that it will keep Bajor out of the coming fight and in turn, war. Rom and Leeta are married by Sisko in his capacity as the Emissary and a Starfleet captain.
As the Dominion fleet approaches, Sisko orders a civilian emergency evacuation of DS9. Starfleet and Bajoran militia personnel remain to defend the station until the mines are completely deployed. Dominion forces attack and are met by DS9's armaments and Martok's vessel, the Rotarran. After the minefield is activated, Sisko orders the Starfleet personnel to evacuate as well.
The Bajoran militia remains aboard the station, as do Quark, Rom, Morn, and Jake Sisko, who intends to serve as a reporter for the Federation News Service while the station is occupied by the Dominion. Prior to surrendering DS9, Kira disables the station's systems. Aboard the Defiant, Sisko is informed that Jake is not aboard and must still be on DS9. O'Brien asks whether or not they should go back for him. An angered Sisko responds that he can't risk the ship and its crew for one person, even if he is his son. "He is a man" Sisko reasons as he slumps back into his seat and says "Maintain current course". On Deep Space Nine, Kira, Odo, and Quark welcome the Dominion aboard the station. Afterwards, Dukat reclaims his old office in Ops, where he notes the baseball left behind â a message to him that Sisko will return. The final shot of the episode and season shows Sisko with a determined glare, his fingers tented in front of his face before an exterior view shows the Defiant and Rotarran circling around to join the massive Federation/Klingon task force, indicating the great Dominion War has now begun.