Sisko, Kira, and Bashir are held in a Maquis camp, but Gul Dukat is not there. Cal Hudson then tells Sisko he is leaving Starfleet to work with the rebels, certain Cardassia is violating the Federation treaty by smuggling weapons into the Demilitarized Zone, and insisting he and the Maquis will do anything to stop them. Sisko offers to help his friend use more peaceful methods, but Hudson refuses, then stuns Sisko and his comrades in order to slip away. Back on Deep Space Nine, Sisko receives little help from Admiral Nechayev, who insists the treaty be upheld. Unwilling to give up on Hudson, Sisko does not report his friend's betrayal, then meets with Cardassian Legate Parn, who blames Dukat for the weapons smuggling. The encounter convinces Sisko that Cardassia is definitely smuggling weapons — but not through Dukat.
The crew finds Gul Dukat and the Maquis hidden on a small planet, and Sisko, Bashir, and Odo take a Runabout to bring him back. A tense standoff ensues, and when one of the Maquis opens fire, Sisko is able to gain control, rescue Dukat, and take prisoners. However, Sisko leaves one Maquis member behind, asking him to tell Hudson that Starfleet knows nothing about his betrayal and he still has time to change his mind.
Upon their return to the station, Sisko tells Dukat that the Cardassians have turned against him. Not surprised, Dukat joins forces with Sisko, offering to help stop the smuggling if Sisko will help him stop the Maquis. Later, Quark, who has been arrested for helping sell weapons to the Maquis, reveals a list of what the group has. Dukat believes the Xepolites are transporting the weapons for the Cardassians, so they soon locate a Xepolite ship and prepare to board it.
Locked in Odo's holding cell with Sakonna, the Maquis' Vulcan liaison, Quark convinces her to reveal the rebels' next step — a plan to attack a weapons depot hidden in a Cardassian civilian population center. Sisko tries to talk to the Maquis one last time, warning them that he will stop their plan. Hudson then arrives, and when Sisko tells him he will be able to stop the Cardassian weapons shipments, Hudson replies that he is determined to fight this war and win anyway, ultimately rejecting Sisko's offer to return to Starfleet.
Dukat learns that the targeted weapons depot is located in the Bryma Colony, then joins Sisko and the senior officers for one last stand against the imminent Maquis attack, taking three Runabouts to stop the group before it gets to the planet. When the Maquis ships finally appear, the initial skirmish results in damage on both sides, leaving only Sisko and Hudson in a final face-off. Sisko successfully stops his friend, then allows him to escape. Sisko returns to Deep Space Nine a hero, but wonders if he has really stopped a war, or merely delayed the inevitable.