Aboard the USS Honshu, Captain Benjamin Sisko thinks about the man he was on his way to visit in the ship's brig. Sisko recalled the doctors' assurances that he would be sane -- they claimed he had made a full recovery. "Maybe I prefer to think of him as a crazy man... a broken man. He'd be less dangerous that way." He then admitted that he felt the prisoner would be better off dead –– however, such thoughts were unworthy of a Starfleet officer. Sisko thought about the losses their prisoner had suffered. "He lost an empire, he lost his daughter, and he nearly lost his mind. Whatever his crimes... isn't that enough punishment for one lifetime?'' Sisko then comes upon the man inside the brig, Gul Dukat.
After some small talk, Dukat engaged Sisko in a discussion regarding the appearance that Sisko will be making before a special Federation Grand Jury. Sisko tries to assure Dukat by explaining that in the Federation, he would be innocent until proven guilty. Dukat then asked Sisko his opinion on Dukat's innocence, but Sisko ducked the question by saying that he had not read all the charges. Dukat then pointed out that it was not like him to equivocate. Sisko informed Dukat that he would not be tried until the end of the Dominion War and that his appearance before the special jury would just be a formality. Still suspicious, Dukat reminded Sisko that he was going to be the prosecution's witness. Sisko tells him, "I'll tell them everything I know."
Sisko then offers his sympathies over the death of Dukat's daughter, Tora Ziyal. Still suspicious of Sisko's motives, Dukat then asked, "Do I detect the fine hand of Dr. Cox at work once again?" Sisko explained that he just wanted to offer his condolences, with Dr. Cox's permission. Dukat realized Sisko was sincere and apologized. Dukat explains that Dr. Cox encouraged him to speak of Ziyal whenever possible, since it was her death that led to his momentary instability. Sisko then informed Dukat that they would reach Starbase 621 tomorrow, and he would see him at the arraignment. As Sisko left, Dukat thankd Sisko, as well as Major Kira Nerys, for caring for Ziyal over the past few years. Sisko then asked Dukat if he could get him anything, and Dukat jokingly asks for one bottle of Kanar and an Orion slave girl. Suddenly, the ship shakes and red alert is sounded.
Kira walks out of Sisko's office on Deep Space 9 and informs the rest of the senior staff that the Honshu was just destroyed by a wing of Cardassian destroyers. She also tells them that so far Starfleet has picked up the distress beacons from three escape pods and one shuttlecraft. The only available ships to search for survivors will be the USS Defiant and the USS Constellation, because of Dominion activity along the border. Additionally, the Defiant will only have 52 hours to search, as it must leave to guard a troop convoy near the Badlands. Despite objections from the senior staff, Starfleet orders stand. Worf orders an immediate departure, but before he departs, Kira reminds him of the deadline.
Sisko awakens and finds himself lying by a campfire in a cavern, with Dukat. Dukat tells Sisko of how they arrived on the planet in the first place – ironically, it seems that Cardassian destroyers shot them down. Sisko was heading to Engineering when a plasma conduit exploded 15 meters down the corridor from the brig, resulting in plasma burns on the left side of his body. Dukat then informed Sisko that he and Lieutenant McConnell found Sisko when the order came to abandon ship. When Sisko was asked where McConnell was, Dukat reveals he died when a piece of shrapnel hit him in the head just as they were carrying Sisko into the shuttle. Sisko is told that the engines for the shuttle were damaged from the shock waves and it is grounded.
Dukat also set up a distress beacon, which was broadcast on a neutral frequency. Sisko agreed this was fair. He finds that his broken arm was held together by an improvised cast that Dukat made, since he did not know how to use the bone regenerator. Dukat excuses himself to search for food, since they only have a week's worth of rations from the shuttle. "What are you planning to do with him?" inquired Weyoun, to which Dukat replied that he and Sisko had a lot to talk about. Weyoun then reminded Dukat about the time spent in the hospital, where he had to be sedated. This leads an outraged Dukat to fire a phaser at Weyoun, revealing only a rock wall with a smoldering hole.
Sisko wakes up to find Dukat preparing soup. The two discuss what happened the previous night and Sisko's bout with nausea, which he apologized for. Dukat assured him the mess was nothing compared to his days as a newly minted Glinn aboard the Kornaire, reminiscing about an incident involving three men in an compartment that had gone through an explosive decompression. Uncomfortable, Sisko tells Dukat to change the subject and in turn, Dukat sarcastically proclaims 'the Emissary has spoken.'
Dukat insists that Sisko should have a sense of humor about their predicament, pointing out the possibility they'll be rescued by the Dominion and commenting on how their universe could be amusing when it allows radical shifts in fortune. Sisko refuses to be humored by their situation, but asks Dukat why he was looking around. Dukat claims it must have been the wind that he heard, offering Sisko a sip of his soup. As the two work on improving the flavor of the meal, they have another conversation regarding Deep Space 9. Dukat asked about Kira, Odo, and Quark, attempting to convince Sisko that they never gave him a chance and that his policies toward the Bajorans were generous. Dukat continued to press, claiming it was his intention to rectify the mistakes between Cardassia and Bajor. Sisko ignores this, and instead inquired about the next ingredient for their soup.
While Dukat adds salt to the soup, he questions Sisko whether or not he'll give him the benefit of the doubt. Sisko responds with a question of his own, asking Dukat if he really does care about what he thinks. Dukat follows up with another question, asking him if he cares about what his friends think of him. Sisko realizes Dukat was implying they are friends, making it clear that they are not friends and even though he is grateful for saving his life, that's as far as it would go. Again, something catches Dukat's attention with Sisko asking him if there is nothing out there. Dukat assures him that it was the wind, but goes out to the caverns to double-check. Somewhere deeper in the caverns, Dukat is arguing with Damar, who attempts to convince Dukat to kill Sisko soon and escape to assist Cardassia in its victory. While Dukat conversed with the Damar delusion, Sisko checks the transmitter and discovers that though the outside display indicated System On-Line, its secondary display on the inside revealed the systems were offline.
When Dukat returns, Sisko tells him there may be something wrong with the com system. Dukat first checks the outside display, reporting the unit to be fine. Sisko suggest that the casing should be taken off and then run a full diagnostic just to be sure. Dukat complies and checks the inside of the transmitter but pretends to run a diagnostic, assuring Sisko then there was nothing to worry about, that the unit is working. Sisko then realizes that it was off intentionally.
Alone in the cave, Captain Sisko worked on the transmitter with one of the tines he had broken off his fork. After some tinkering, Sisko managed to have the unit's systems back on-line to restart the Distress signal. Hearing Dukat's approach, Sisko diligently covered up his work and hid his altered fork underneath his sheet. Dukat returns with a couple of cushions salvaged from the shuttle, shining his flashlight on Sisko who appeared to have just woken up. As Dukat helps Sisko get settled against his new cushion, the Captain comments that it appears he is planning a long stay. Dukat explains that he only wants the both of them to be comfortable as they await for a rescue.
Once Dukat settled upon his own cushion, he told Sisko about an idea that occurred to him while he was out at the shuttle. Dukat muses about how confused the Bajorans would be if they found both of them sharing the same hardships, calling himself the evil Gul Dukat, and Sisko the Emissary of the Prophets. Dukat points out that it is just the two of them, all alone, that no one is there to judge them, insisting that they both be honest with one another. He presses Sisko for his opinion on him, but is interrupted by another figment of his delusions, in the form of Kira, who whispers an opinion of her own over his shoulder. She tells him that she thinks he is an evil, sadistic man who should have been tried as a war criminal years ago – put up against a wall and shot. Having heard her opinion, this prompts Dukat to question Sisko if he agrees with Kira on how he feels about him. Sisko tells Dukat that he doesn't see any reason in discussing the matter any further. Dukat disagrees and continues, telling Sisko that his name and reputation have been slandered and twisted after the Occupation of Bajor. He states he has been wrongfully vilified throughout the Alpha Quadrant for six years and wonders out loud if Sisko is one of those people. Sisko insists that he could not really pass judgment on him because he was not there during the Occupation, nor did he see the things that Dukat had to struggle with day after day.
The Kira delusion warns Dukat that Sisko does not want to tell him the truth because it would upset him. Sisko watched as Dukat talked over his shoulder at the air, realizing that Dukat is delusional. Dukat believes that Sisko was not being entirely honest, pointing out that he was not a man who hesitates to make snap judgments when the situation calls for it. Sisko tells Dukat he is right about being judged unfairly, that he himself judged Dukat unfairly, and that he probably had good reasons for everything he had done on Bajor. Dukat agrees with Sisko, and claims that some of his harsher acts were forced upon on him by Central Command. He then explained to Sisko that he wanted to use entirely different tactics with the Bajorans, that he wished to have ruled with "a softer hand." Sisko tells Dukat that he understands, stating that he was a soldier and was only carrying out orders. Dukat eagerly agrees with this assessment only to laughed at by the Kira delusion, calling him a fool, telling him he is being patronized. After Dukat yells at his delusion. Sisko manages to turn Dukat's attention onto him, suggesting that they ignore Kira and pretend she is not there. As the Defiant picks up a distress signal and beams up two additional Honshu survivors, Dukat fires his phaser wildly at his Kira delusion.
Dukat later discovers Sisko's hidden fork and notices one of its missing tines, concluding after he checks the transmitter that Sisko had repaired the unit behind his back. Outaged, Dukat destroys the transmitter which cuts the signal the Defiant picked up moments earlier, and from the debris of the transmitter he dislodges a metal bar, which he uses to assault Sisko.
Despite subspace interference over the viewscreen, Kira reminds Worf to follow his original orders to end their search soon so they can assist the troop convoy in the Badlands. Both Doctor Bashir and Miles O'Brien disagree with the Major's orders, wanting to pretend they were unable to understand the message. Worf tells them that they all understood, and ignoring them would be dishonorable. Worf dismisses Bashir from the bridge, and he ordering helm to lay in a course for the third planet and continue their search for the remaining time.
Sisko awakens with his head bleeding to see Dukat standing over him wiping blood from a metal pole in his grasp. Dukat tells Sisko that he brought the damage upon himself, with the groggy captain making a mention of victims that must have suffered like him. Dukat begins to name all the things he has been called, sarcastically calling Sisko a "supreme arbiter." A frustrated Sisko demands what Dukat wants from him and Dukat explains that he does not want any pretenses, only that they express their true thoughts. Sisko takes Dukat up on his challenge and begins a fierce barrage of questions – true and false, of Dukat's role in the Occupation. The murder of over five million Bajorans on his watch is Dukat's responsibility. Dukat adamantly claims otherwise, explaining that he tried to save lives during his administration. Sisko then demanded for evidence.
Dukat says the Occupation had already been going on for almost 40 years, but the planet was not ready for full-scale colonization. He tells Sisko that Central Command wanted the situation resolved and they didn't care how it was done. Dukat reminds Sisko that he wanted to use "a gentler hand" when dealing with the Bajorans – reducing the output quotas by 50 percent. Dukat begins to list orders he gave during his tenure, such as reorganizing the camps, abolishing child labor, improved medical care, and food rations were increased as the death rate decreased by 20 percent. Dukat also explains that he had to punish the Bajorans as well: on his anniversary, an orbital drydock was blown up, killing over 200 Cardassians. He then rounded up 200 Bajoran Resistance members, and executed them, claming it was justice, not malevolence. He also executed more Bajorans after a failed assassination attempt.
As Dukat continued his stories, the delusions in the forms of Weyoun, Damar, and Kira all support his every word. When Dukat asks Sisko if he understood what he said, Sisko pretends to have been moved by his stories and explains that what happened to the Bajorans was not Dukat's fault, it was theirs. Dukat eagerly agrees with Sisko's empty revelation as Sisko plays along, asking Dukat why the Bajorans did not appreciate the rare opportunity he offered. Dukat accused that Bajorans were small-minded, ignorant fools, that the Cardassians were clearly the superior race, and they did not choose to be so – fate handed them that role.
Ultimately, Dukat confesses his hatred for the Bajorans and everything about them, from their religion, Bajoran earrings, and their broken, wrinkled noses. He is most infuriated by their wishes for equality to the Cardassians. Sisko, still playing along, suggests to Dukat that maybe he should have killed them all. Dukat agrees entirely, proclaiming he should have "turned their world into a graveyard in which the likes the galaxy has never seen." From over his shoulder, Sisko struck Dukat behind with the same metal pole and acidly finishes their conversation, "And that is why you're not an evil man."
Sisko finds his way to the shuttle through a sandstorm, discovering that it is still operational. Just as Sisko begins to depart, Dukat attacks Sisko and a fight ensues. Dukat then forces Sisko out into the sandstorm while brandishing a phaser. Before Dukat departs, he thanks Sisko for their time together promising, they will not be seeing each other for awhile, and that vows "from this day forward, Bajor is dead! All of Bajor" As the doors to the shuttle door close, Dukat along with the rest of his delusions, Weyoun, Kira, and Damar smile over an unconscious Sisko lying in the sandstorm.
Dax wakes Sisko, reporting that she notified Starfleet of Dukat's last known position and that they'll find him. Sisko disagrees about the possibility of his capture and begins to discuss life, about how it seems complicated and that it appears everything is a shade of gray, that there is nothing truly good or evil. He then explains to Dax that after he spent time with a man like Dukat, he realized there that there is true evil. Dax points out that realizing truth is one thing, but to do something about it is another. Sisko makes it clear about what he will not do; he makes a vow to stop Dukat from destroying Bajor.