Bashir is surprised when his "friend" Garak, a Cardassian tailor, is attacked and bitten by a Cardassian boy who is visiting the station with his Bajoran father. The boy, Rugal, is an orphan abandoned after the war who was adopted by a Bajoran family. No sooner does Bashir tell the crew about the incident than Cardassian leader Gul Dukat contacts Sisko asking him to investigate. He claims any information will help in his quest to bring the Cardassian war orphans back home. Sisko begins by speaking to Proka, the boy's Bajoran father, who tells him that, while he has been honest with Rugal about the Cardassians and their atrocities, he loves Rugal as if he were his own child. This is contradicted by an alien named Zolan who was with the pair when the incident occurred. He tells Bashir that Rugal has been mistreated by his adoptive family and forced to hate himself for his heritage. Proka vehemently denies this, but Sisko insists that the boy be taken into station custody.
Later, Bashir discusses the situation with Garak while tending to his wounded hand. Garak laughs when he learns that Gul Dukat is claiming to want to save Cardassian war orphans and implies that Dukat is lying, indicating that he was in charge of the very operation that left those orphans behind. Bashir promptly brings this information to Sisko, who happens to be in the midst of a conversation with Dukat about the possibility of returning Rugal to Cardassia. Bashir boldly interrupts and asks Dukat why he left the orphans on Bajor, and Dukat responds that the civilian leaders ordered it. Unsure who to believe, Sisko requests a meeting with Garak, who proceeds to deny ever saying anything about Dukat to Bashir. Bashir follows Garak out and confronts him about his lies, and he angrily tells Bashir that the information he shared was confidential. Meanwhile, Rugal moves in with O'Brien and Keiko, and soon reveals to O'Brien that he hates the Cardassians and hates being one. He says that while his parents also despise his people, they love him and have never mistreated him.
That night, Garak wakes Bashir up and says that they must go to Bajor immediately. Bashir approaches Sisko for approval to use a Runabout just as Gul Dukat sends a communication to Sisko stating that Rugal is the son of Kotan Pa'Dar, one of Cardassia's most prominent political figures. Pa'Dar is en route to retrieve the boy and take him home to Cardassia. Still confused, Sisko lets Bashir travel to Bajor with Garak to investigate. While visiting an orphanage, Garak accesses and downloads all of the region's computer files on orphan resettlement, but is initially unable to find any record of Rugal.
On route back to Deep Space Nine, Bashir grows suspicious of Garak and questions him about what is going on. Garak indicates that Pa'Dar and Dukat are political enemies, and that Dukat's interest in the boy is suspect. Pa'Dar soon arrives at the station and goes in search of his son, but first encounters O'Brien, who warns him of the boy's negative attitude toward his heritage. Pa'Dar replies that losing his son was a terrible tragedy and he is determined to bring him home, but when he meets Rugal, the boy angrily refuses to go. Proka insists on retaining custody, and Pa'Dar turns to Sisko to mediate the situation just as Gul Dukat makes his unexpected arrival at the station.
Dukat, Pa'Dar, Proka, Rugal, and Sisko meet to decide who should get custody of Rugal. Sisko is suspicious that Dukat has come so far for a simple custody hearing, especially since he and Pa'Dar have been political enemies. However, Garak learns more about Dukat's motives when he realizes that Rugal's name has probably been deliberately erased from the orphan resettlement files. He tracks down the Bajoran official who originally wrote the file and learns that Rugal was brought from Terok Nor, which was the space station's name under Gul Dukat's command. Apparently, Dukat deliberately left Rugal behind in hopes of someday using this to humiliate his adversary, Pa'Dar. When Sisko learns of this, he decides to let Pa'Dar take Rugal back to Cardassia despite the obviously distraught boy's unwillingness to go, realizing that the innocent father has a right to attempt to raise his child.