Dax, Garak, Odo and Sisko are en route to Deep Space 9, having attended a conference geared towards a "dispassionate historical view" of the Cardassian Occupation of Bajor. Garak indignantly claims the Bajorans present ignored every argument he made, but everyone agrees Odo was the highlight of the conference due to his reputation for fairness despite working for the Cardassians during the Occupation. However, Odo appears uncomfortable with the discussion.
The runabout arrives at Deep Space 9, where its four occupants are found in a comatose state, their life signs weak. Doctor Bashir tries to awaken them, to no avail. In the infirmary, he explains to Worf that the runabout encountered a plasma storm, a relatively common phenomenon. Unfortunately, Bashir cannot explain what has happened and goes about researching the issue.
Meanwhile, the unconscious crew members have awoken on the Promenade in a time when the Cardassians still controlled the station, Terok Nor. Even stranger, people around them seem to think the Human, Trill, Cardassian and former Changeling are all Bajoran. Gul Dukat and Odo's predecessor, security chief Thrax survey the area from the second level. Odo begins to hallucinate as the others talk, seeing a dead Bajoran man, shot in the chest with a phaser, walk by. Soon a Cardassian officer arrives to take Dax, who has been selected for "questioning". When Garak tries to stop the man, he gets a bloody nose for his trouble.
Back in the infirmary, Garak's nose begins to bleed. An alarmed Bashir explains that the brain can have a powerful effect on bodily functions. There is some odd psychosomatic activity in Garak's brain, but Bashir cannot risk interrupting whatever is happening for fear that one of the patients will be injured or even killed.
As usual, there is a purpose to everything Garak does; once he, Odo and Sisko are alone, he explains that he "borrowed" a scanning device from one of the guards when they took Dax. He uses it to find their Bajoran identities. Sisko is Ishan Chaye and Garak is Jillur Gueta, but Odo seems to know this already and identifies himself as Timor Landi. Before Sisko can question him about the issue, Quark arrives with a pair of guards and offers the three of them work at his bar.
The other soldiers take Dax to Dukat's quarters, where there is awkward silence as he looks her over and has her pour him a bottle of kanar. He claims he is misunderstood and wants a "friend" with whom to share his innermost thoughts. Although Dax's position is not an enviable one, it is clear her predicament could be far worse.
As Dax learns about Dukat's apparent penchant for Bajoran women, Garak learns what it is like to be a Bajoran laborer cleaning Quark's bar alongside Sisko and Odo. The experience seems to humble him somewhat, although he retains his Cardassian mindset about the Bajorans being better suited for such tasks. Odo has another hallucination of the Bajoran man he saw previously and two other men, and though he claims his visible discomfort is from the smell of the chemicals he is using, Sisko uses the chance to bring up Odo's apparent familiarity with their Bajoran aliases. It is revealed that Ishan, Jilur and Timor were innocent Bajorans executed for an assassination attempt on Dukat's life.
The trio try to come up with a plan of escape, and while they do, Thrax enters to discuss various things with Quark. Garak recognizes a name, Livara, as a Romulan spy; however, according to his stolen data pad, Livara would have been visiting Terok Nor seven years ago, at which time Odo was serving in Thrax's place. This only leads to more unanswered questions.
Later on the promenade, Sisko uses a trick he once learned from Major Kira to subtly request a meeting with the Bajoran Resistance, turning over a vase at one of the shops. They then get some soup and sit at a nearby table to wait. Things become even stranger for Odo as his hands are suddenly covered in blood; however, no one else can see it, and it disappears shortly. A Bajoran man from the Resistance joins them and Sisko tries to arrange transport off the station. Before he can finish, there is an explosion nearby where Gul Dukat is walking with Dax and his entourage. As the Bajoran man leaves, Sisko instinctively runs over to see if Dax is okay. However, he, Garak and Odo are arrested and taken to a holding cell.
Thrax visits the brig that evening to inform various prisoners of their fate. Under Cardassian law, the verdict is reached before the trial begins, and Sisko and the others are to be sentenced the following day. Odo desperately pleads with Thrax, knowing they are innocent, but the Cardassian officer refuses to refute the circumstantial evidence, claiming the Bajorans need to accept their fate.
Back in Dukat's quarters, he drones on about how lenient he is with the Bajorans and how he sees them as his children. Dax is obviously uninterested but pretends to listen. Waiting for an opportunity, she knocks the Cardassian upside the head, rendering him unconscious.
Each of the accused deals with the predicament in his own way. Garak plans an elaborate web of stories as usual in order to try to convince the Cardassians of his true identity. Odo continues to act strangely, but Sisko once again tries to connect the dots, as everything so far has pointed to the constable. Sisko theorizes that Odo knows more than he thinks he does, but once again the conversation is interrupted – this time by Dax, who burns a hole in the door of the brig.
The four of them head for an airlock and Dukat's personal shuttle. Dax reveals that she has used her knowledge of the station to ensure the Cardassians will be unable to stop them from leaving. Several soldiers follow suit and a fight ensues, with Thrax facing Odo. Once the other soldiers have been subdued and Thrax appears trapped, he turns into a metallic liquid form (the hallmark of the Changelings) and escapes through an air duct. Pressed for time, they continue moving towards the shuttle but find themselves back in the holding cell, two hours prior to their execution.
Thrax enters and honors Odo's previous request for an audience, taking him to the security office in the next room. There Odo attempts to reason with him, citing evidence that will prove their innocence. Thrax is more interested in order and believes the Bajorans need to accept their place in history, but when Odo reveals that the four of them do not belong there, Thrax reveals that he knows.
Suddenly, Odo and the others find themselves on the Promenade, lined up and prepared for execution. His conscience visibly takes over as he tries to fight Thrax, claiming he will not "let this happen again", and the scene again changes; Sisko, Dax, Odo and Garak are now dressed normally. A distance away, the three Bajorans Odo saw earlier are lined up for execution – with Dukat and another Odo (dressed in Thrax's uniform) standing nearby. Odo reveals that another identical bombing occurred three days later and if he had performed any kind of investigation instead of relying on circumstantial evidence, then he would have seen that the three men were clearly innocent. However he didn't know the difference between "order" and "justice" and he allowed the three innocent men to be executed as an example. The Bajorans are summarily shot with a phaser, after which the scene slowly disappears and they awake in the infirmary.
Baffled and intrigued, Bashir explains that some of Odo's morphogenic enzymes were apparently left over from when the Founders forced him to remain a Solid. The events were triggered when the runabout flew through the plasma field which triggered the enzymes causing Odo to (subconsciously) reach out for others with whom to form a link, the end result being a telepathic experience brought on by Odo who was thinking about the three Bajorans at the time. "It would make a fascinating paper," he observes, but seeing Odo's reaction, adds, "although I don't intend to write one." Just then Kira walks in, and it's clear to Bashir that he should leave the two alone. After he leaves, Kira tells Odo that even though it's been two days she still can't believe what she read in his report. She tells him that as far as the Bajorans were concerned, he was different. He stood apart from the brutal Cardassians and that made him special. But she also knows that she did things during the Occupation she'd rather forget, but she needs to know from Odo that no other innocent people died on his watch. Odo honestly replies that he doesn't know... but he sincerely hopes not.