The USS Honshu is transporting Gul Dukat to his war crimes investigation. Sisko is also onboard and goes to see the former Cardassian leader who is being held in the ship's brig. Dukat, who suffered a nervous breakdown over the death of his daughter, assures Sisko that he has recovered. Suddenly, the ship is ambushed by Cardassian warships. During the attack Sisko is seriously injured, but Dukat, who is released from his cell, is able to get him to a shuttlecraft. They manage to escape to a nearby planet where he tends to Sisko's wounds. When Sisko regains consciousness, Dukat informs him that they are stranded and he is sending out a distress signal.
Unbeknownst to Sisko, Dukat hallucinates encounters with Weyoun and Damar, who advise him to kill the Starfleet captain. Dukat reveals that he intends to - after Sisko shows him the respect he deserves. While Dukat "talks" with his colleagues, Sisko notices that the communications system is, in fact, not sending out a signal. When Dukat returns, Sisko tests him by asking him to check the system. He does, telling Sisko the unit is working fine.
Meanwhile, Worf searches for Sisko in the Defiant, but has limited time before he must leave to escort a convoy of Federation ships. Sisko adjusts the communications system while Dukat is out, but must stop when he returns and "play along" while Dukat defends his treatment of the Bajorans. When Dukat starts "arguing" with Kira, Sisko realizes something is very wrong. He pretends to agree with Dukat, and the ruse almost works until Dukat notices that the distress signal is now on-line. He destroys the com system and attacks the defenseless Sisko.
On the Defiant, Worf runs out of time and must leave to escort the convoy, but continues searching a bit longer. Meanwhile, Dukat continues to push Sisko for his approval. Bruised and battered after Dukat's attack, Sisko invites him to talk about his experience with the Bajorans. Dukat continues to insist his benevolence and good will towards Bajor but Sisko argues against him, berating him for his hypocrisy and self-deception. Finally, Dukat is forced to admit this, screaming out that if he had his way he would kill all Bajorans. Using this distraction, Sisko knocks him out with a metal bar and, despite his weakened condition, escapes to the shuttle.
Dukat recovers and follows Sisko outside, tackling him to prevent his escape. But when Sisko challenges his enemy to kill him, Dukat instead leaves Sisko behind and takes off in the shuttle, vowing to destroy Bajor. The Defiant crew then picks up Dukat's signal and finds Sisko. Dukat, however, escapes, leaving Sisko grimly aware of the battle over Bajor that is sure to come.