Calvin Hudson, now part of the Maquis, has Sisko, Kira, and Bashir at his mercy. Sisko demands to see Gul Dukat, whom the Maquis abducted, to which Hudson accuses Sisko of siding with the Cardassians over him. According to Hudson, the Maquis's top priority is peace but insists the Cardassians' crimes cannot go unpunished, and Sisko points out that it is revenge, not peace, they seek. "I prefer to call it retaliation," Hudson smirks. After Sisko declines an offer to join the Maquis, the Maquis shoot him, Kira, and Bashir.
Admiral Nechayev is waiting for Sisko when he returns to Deep Space Nine, and Dax informs him that Legate Parn of Cardassian Central Command will be arriving soon as well. Necheyev refers to the Maquis as "a bunch of irresponsible hotheads" and tells Sisko to talk to them, although he finds such sentiments out of touch with reality. When Necheyev leaves, Kira informs him that Legate Parn has just arrived. He is on his way to greet the Cardassian leader when Odo reports that he has caught "one of the Vulcan's accomplices."
Sisko arrives in the security office to find Quark in a holding cell. Quark attempts to evade discussion of his business with Sakonna but eventually reveals that he arranged for the Maquis to acquire weapons. While he had not heard of the Maquis at the time, he is sure Sakonna plans to execute her plans within the next few days. Legate Parn upon meeting with Sisko informs him and Kira that the Cardassian Central Command has discovered Dukat to be the leader of "a small group of misguided officers" who were smuggling weapons to the demilitarized zone. However, neither Sisko nor Kira believe him.
On one of the Maquis worlds, Sakonna attempts to establish a Vulcan mind meld with Dukat, who openly mocks his captors. When Sisko, Bashir, and Odo interrupt the interrogation, there is a momentary standoff, during which Dukat grows impatient. "Shoot them!" he yells and knocks Sakonna over, triggering a firefight. The Maquis are arrested, but Sisko allows one of them named Amaros to go free with a message to Cal Hudson that it is not too late to settle things peacefully.
They bring Dukat back to Deep Space Nine, where he inquires about the fact that Federation not Cardassian forces rescued him. Sisko tells Dukat about Legate Parn turning him into a scapegoat and the two men put past differences aside to work together to stop both the weapons smuggling and the Maquis. By this time, Odo has obtained an extensive list of weapons Sakonna bought from Quark, but he has been unable to find out more. The crew focus on the weapons smuggling instead for the time being. With Dukat's help, they find a Xepolite trader and detain a shipment of weapons from him, finally obtaining proof of the conspiracy.
Back on the station, Quark and Sakonna share a holding cell. He calls her position with the Maquis illogical and uses the Rules of Acquisition to explain that with the Cardassian plan exposed, "peace can be bought at a bargain price." She informs Sisko that the Maquis are planning to blow up a hidden Cardassian weapons depot in the next 52 hours, but she does not know where it is. Dukat says he can find the depot's location, and in the meantime, Sisko visits cal Hudson one final time. He brings along Hudson's uniform, which Hudson vaporizes with a phaser.
The crew is waiting in runabouts when the Maquis arrive at the depot, and as neither Hudson nor Sisko wants to hurt the other, the resulting dogfight is relatively slow paced. Sisko's runabout and Hudson's raider each try to disable the other. Hudson manages to knock out Sisko's engines, but his own phasers are disabled. He flees and, over Dukat's objections, Sisko allows him to escape. Ultimately, Sisko wonders if he has prevented a war or delayed the inevitable.