Kira is surprised when she sees records indicating that she was incarcerated at Elemspur, a Cardassian prison, 10 years ago. Certain she was never at the prison, Kira tracks down a man listed as her one surviving cellmate. The stranger claims to remember Kira, but she has no idea who he is and decides to learn the truth. Kira departs for Bajor, but is kidnapped, waking up on Cardassia, where an official named Entek tells her she has been brought home. Looking in a mirror, Kira is horrified to see that she now looks like a Cardassian.
Entek gently tells her she is Iliana Ghemor, a field operative of the Obsidian Order who volunteered for an undercover assignment on Bajor a decade ago. The Cardassians captured the real Kira, gave her memories and appearance to Iliana, then sent the replacement back to Bajor to infiltrate the resistance. Entek leaves, giving the disbelieving Kira a data rod containing a personal message Iliana recorded before she left. Soon afterward, Legate and Central Command member Tekeny Ghemor arrives, claiming he is her father and they are in his home. Kira dismisses him, and is surprised when he seems genuinely hurt that his daughter's suppressed memories haven't yet returned.
Back on Deep Space Nine, Garak reveals that Kira may be held by the Obsidian Order. Sisko decides to go to Cardassia and find her, forcing Garak to join him and Odo. On Cardassia, Ghemor tries desperately to jar Kira's memory of her life as his daughter, but she refuses to either believe him or trust his intentions. Entek attempts to interrogate Kira, saying they need information from Iliana's mission, but is frustrated that her memory is not resurfacing. Entek then shows her a younger Kira's dead body, which has been cryogenically preserved, looking just like it did in the prison record.
Kira believes the body to be a fake, but Entek then speaks of experiences she has never told another person. For the first time, Kira begins to doubt herself, but she doesn't give up and decides to escape, only to have Ghemor catch her. Later, Entek returns and begins to interrogate her yet again. An angry Ghemor comes in and dismisses Entek, invoking his status with the Central Command, then tells Kira that, even though it will break his heart, he will get her away from Cardassia.
As the final arrangements are made, Ghemor reveals that he is a dissident. This puts the pieces of the puzzle together for Kira. She realizes that Entek is not really after her, but is only using her resemblance to Ghemor's daughter to get him to betray the Central Command. Entek then enters with two Obsidian Order agents who surround Kira and Ghemor. But Sisko, Garak, and Odo appear and stop them, with Garak killing Entek in the process. Ghemor returns with Kira to Deep Space Nine, where tests prove she is Bajoran. Ghemor vows to find his real daughter, but also tells Kira that, until then, she is the closest thing to family he has.