Doctor Bashir sits down at his usual table at the Replimat with Garak, and once again tries to figure out if Garak is a spy on the station. Garak laughs it off, as he always does. When a young Cardassian boy, wearing a Bajoran earring and escorted by a Bajoran man, sits down near them, Garak cannot resist commenting on it. He goes over to the man and says what a nice boy he has. The boy bites Garak's hand, and shies away.
After making sure Garak's hand is not severely damaged, the doctor reports to ops, and tells the senior staff about it. Everyone is baffled. That's when Gul Dukat calls on subspace to ask about the incident. When Commander Benjamin Sisko skeptically asks Dukat how the news reached him so quickly, Dukat changes the subject. He says the boy is one of the many war orphans left behind when the Cardassians left Bajor. He asks Sisko to investigate this incident, since he is trying to get the orphans returned to Cardassia. Sisko agrees.
First, Sisko talks to the father, Proka Migdal. He is agitated at first, thinking that Garak filed a compliant, and they want to arrest him. When Sisko explains they just want to talk, he relaxes slightly. He wishes that the Cardassians would have paid as much attention to his boy then as they want to now. He insists that he adopted Rugal so that Rugal wouldn't have to suffer for the mistakes of others, and that Garak should have minded his own business. The Doctor points out that the boy was terrified of Garak, and that he was probably raised to hate Cardassians. The father agrees that Rugal hates Cardassians, because the facts alone would -- and should -- make him hate Cardassians. He loves his son, just as if he were his own flesh and blood, and considers him a Bajoran.
Continuing the investigation, Doctor Bashir talks to Zolan, a trader who knows the family well. He is evasive, but when the Doctor presses him, he explains that he had visited the family a few times when the father was looking for a new job. He tells Bashir that Rugal is being raised in a terrible way - being told every day that he is horrible for being a Cardassian - and that the parents are taking out their revenge against all Cardassians on the boy. When Sisko and Bashir confront the father, he is outraged, saying he has done nothing. Sisko accepts his word, but has Rugal stay with Keiko O'Brien for the time being.
Rugal says he didn't do anything wrong when his father brings him out. He is nervous, but finally goes with Sisko and Bashir when the father says they won't hurt him, because they're Human, not Cardassian.
Back in sickbay, Doctor Bashir heals Garak's hand, and mentions Gul Dukat's attempt to resolve the war orphan predicament. Garak laughs and begins a line of questioning of his own. He plants in Bashir's mind that Dukat's story should not be believed: Dukat was in charge of the withdrawal from Bajor, therefore it is his fault that the children were left behind, so why is he trying to get them returned home?
Back in ops, Sisko is telling Dukat that it may not be very simple to send Rugal back to Cardassia. When the doctor arrives, Sisko asks Dukat to look up the boy's DNA to search for any surviving relatives, in case he does decide to send him home. Dukat agrees, then Doctor Bashir interrupts. He asks Dukat why he chose to leave the children behind. Dukat is not pleased, and explains that he was ordered to do it by the civilian leadership of Cardassia and had no choice. Bashir corrects him, and states that the civilian leaders do not have such detailed control of the military. When Dukat asks where he got this information, he admits it was from Garak. Dukat tells Bashir to tell Garak he had no choice, and cuts off the viewscreen.
Sisko asks why the doctor presumptuously interrupted his conversation with Dukat. Bashir explains that Garak thinks Dukat is lying - which he had to deduce, since Garak doesn't actually tell him anything. Sisko is not pleased, but lets him off with a reprimand.
Meanwhile, in the O'Briens' quarters, Rugal asks Chief Miles O'Brien what will happen to him. O'Brien asks if it's hard on him being Cardassian. Rugal becomes defensive, saying he was born that way and it isn't his fault. The Chief rephrases his question: "Isn't it hard to live with people who hate you?" Rugal answers that his parents hate other Cardassians, not him, and they have done nothing wrong to him. When he asks what Miles thinks of Cardassians, the chief explains that he can't generalize an opinion about an entire race - he has met Cardassians he didn't like, and Cardassians he did like. Rugal doesn't understand how the chief could feel that way, since the Cardassians killed 10 million Bajorans, and wishes he were Bajoran.
In the middle of the night, Garak sneaks into Bashir's quarters and says that they need to go to Bajor now. The Doctor wakes Sisko up and tries to explain, not very coherently, that he and Garak need a runabout right away to go to Bajor for something important, which Garak won't tell him. At the same time, ops informs Sisko through the com that there is a communication for him from Gul Dukat. He informs Sisko that the boy's DNA has identified him as the son of a prominent politician, Kotan Pa'Dar, who is still alive - so the boy is actually not an orphan. Pa'Dar is heading to the station to reclaim him. Sisko repeats that it's not that simple; the boy wants to go back to Bajor, and he won't send him to Cardassia against his will. Pa'Dar will have to wait for the investigation to finish. Bashir points out that Garak's urgency and the news about Pa'Dar can't be a coincidence, and Garak must know something. This convinces Sisko to give them the runabout.
The two of them head down to an orphanage for Cardassian children and ask about Rugal. The person in charge says that since Rugal's adoption occurred eight years ago, when the Cardassians were still in charge, she probably doesn't have the information. Garak responds with a correction that Cardassians always keep meticulous records, and if they would let him use their computer, he might be able to find the file. When she says that the government hasn't had the resources yet to repair her computer system isn't working, he offers to fix it.
After repairing the computer, Garak downloads the records for all of the provinces into a data clip. This makes Bashir skeptical again that he isn't a spy. On their way out, Garak has to regretfully inform several Cardassian children that, no, he has not come to take them home.
When they are in orbit, Dr. Bashir gets tired of being strung along. He has has the computer shut down the runabout's engines and demands that Garak tell him what's going on or they will sit there until they rot. With that ultimatum, Garak plays another round of 20 questions. He helps Bashir put it all together: Pa'Dar was one of the most notable civilian leaders at the time, and was involved in the decision to evacuate Bajor; Gul Dukat lost his job as prefect when that happened, so he hates Pa'Dar; and now, mysteriously, this boy turns up, and Dukat coincidentally finds out it is Pa'Dar's long lost son.
Pa'Dar shows up on the station, and Chief O'Brien talks to him before he sees Rugal. He explains that the boy hates everything he is, and probably won't react well to see him. Pa'Dar insists that he is the boy's father, so all of that will change. He explains that on his son's fourth birthday, a bomb blew up their house, and the father was convinced he was dead. Family is very important to Cardassians, he says, and he has come here despite the disgrace it will bring him (because there is no excuse for "losing" a member of his family) for that reason. When Rugal walks in, he is scared and stunned. He doesn't remember his father's face, and wants nothing to do with him, despite his father's pain and explanation of what happened. He says his father deserved his pain, and that his son is dead; he will never go back to Cardassia.
The next fight is between Pa'Dar and Proka. He demands that no Bajoran court rule on the custody hearing. After some loud words, Sisko suggests an arbitrator, and both suggest him. He accepts. That's when Odo informs him that Gul Dukat has just arrived on the station.
Dukat explains he has come to observe the hearing, because there is great interest in the case at high levels of the Cardassian government. He wants to see Rugal reunited with his father. He says the disagreements between he and Pa'Dar are not relevant; it is the children who are important. Since Sisko is trying to stall for time to give Bashir and Garak more time to search the files, he asks Pa'Dar go over the events from eight years ago again.
The Doctor and Garak, however, aren't having any luck. Garak soon realizes it is because Dukat probably purged the file on Rugal, since there was something in it he didn't want anyone to see. So, he looks for - and finds within seconds - the person to created the file, Jomat Luson.
While Sisko asks Rugal what he remembers about his adoption and gets nothing, the Doctor and Garak talk to Jomat. She remembers Rugal well, because his case was very unusual. Bajorans usually brought in the Cardassian children from the streets, but Rugal was turned in by a female Cardassian military officer, who was attached to Terok Nor. Also, the officer knew the child's name. Garak helps the Doctor put together the last pieces, and they go to the hearing.
With Sisko's permission, Bashir asks several questions. He gets O'Brien to reiterate the humiliation Pa'Dar is feeling, and when asked, Pa'Dar says it will be the end of his career when it is revealed to the people. Not only that, but the timing is very bad, considering there is an inquiry about to begin concerning an attempted military coup on Bajor. It just so happens that Dukat is one of the key witnesses in that inquiry.
Dukat objects, and says it is irrelevant. Bashir quickly changes his line of questioning, and asks Dukat if he has ever been to the orphanage center where Rugal was adopted. He says no. That center, he explains, is located where Pa'Dar was living eight years ago. Rugal was brought in by a female Cardassian military officer, who seemed to know the child. Perhaps she knew he wasn't an orphan. When Dukat says he knows nothing about that, Bashir points out that she was attached to Terok Nor. The question for Dukat was: Who was the commanding officer of Terok Nor eight years ago? Dukat walks out; he was that commanding officer.
Pa'Dar thanks Sisko for salvaging his political career; Dukat will not make these events public, so this is a stalemate instead of a great loss. With a few words of encouragement from Miles O'Brien, Rugal goes with his father, hesitant, but willing. When the Doctor asks Garak why he helped to defeat Dukat, he is evasive as usual. If you can find all the details, he says, you can put it together yourself.