Major Kira comes across a computer file that contains prison records. It lists her as a prisoner at a Cardassian facility ten years earlier. Having never been in prison, she decides to look into the matter. On her way to Bajor she is kidnapped.
Kira awakens on Cardassia and is welcomed home. When she looks in a mirror, she is shocked to see that she looks like a Cardassian. A Cardassian man visits her and tells her she is his daughter, Iliana, and that he will help her recover her memories. The man, Tekeny Ghemor, describes how she joined a long-term undercover operation with the Obsidian Order. She was surgically altered to look like a captured Bajoran militia member named Kira Nerys, and had her memories blocked and replaced with those of Kira. She was then sent to Bajor in Kira's place to act as a spy. Her mission is done and Ghemor tenderly welcomes her back to her home and family.
Kira will have none of it. She is certain of who she is and is disgusted to think of herself as a Cardassian. When she is shown the dead body of a Bajoran named Kira Nerys, she insists it is a fake. Still, she begins to have doubts. Despite her confusion, she hangs onto her identity and tries to escape. The Cardassians want to probe her for the information she gathered during Iliana's mission masquerading as Kira, and she is quickly caught.
Ghemor is distraught that his daughter does not remember him. He offers to help her escape to avoid harsh interrogations that the Obsidian Order will certainly inflict on her to extract the information. Ghemor is immediately taken into custody by the Order. It is now clear that the Order was using Kira to get Ghemor to reveal himself. By making him think he had his daughter back, they were able to get evidence that he was a dissident.
Odo, Garak, and Commander Sisko arrive in time to prevent the Order from taking Kira and Ghemor away for punishment. Back at Deep Space Nine, tests reveal that Kira is definitely Bajoran. Ghemor understands that she is not really Iliana, but is still sad to bid her goodbye.