Major Kira is contacted by Alenis Grem, a Bajoran archivist who has discovered a computer record of Kira's time in a Cardassian prison camp; Kira is naturally skeptical, as she was never in Cardassian detention, but the records appear authentic. Arranging a meeting with Alenis to examine the files personally, Kira leaves for Bajor. She never arrives; Alenis then contacts the Station, telling them that nobody has seen Kira since she left the spaceport for the former prison camp.
Awakening in a darkened room, Kira is warmly welcomed 'home' by Entek, a Cardassian official. When she looks in a mirror, she is shocked to see that she has been surgically altered to appear Cardassian. Furiously rejecting any notion that she is Cardassian, Kira is introduced to Tekeny Ghemor, an officer of the Central Command, who claims that she is his daughter Iliana; Entek explains that she is a 'sleeper agent', altered to appear Bajoran and placed in a position of authority with the Federation as part of a long-term covert operation.
Ghemor is upset that his 'daughter' doesn't remember him, but is reassured by Entek that her memory will return, given time. Kira is upset and incredulous; when shown the corpse of a dead Bajoran woman named Kira Nerys, she declares the woman's body a fake, but begins to doubt her own memories. When Ghemor compares Kira to her (supposed Cardassian) mother, Kira angrily replies that her (real) mother starved to death in a Bajoran prison camp.
After several escape attempts, she is interrogated by the Obsidian Order, though she provides them with false and misleading information. Eventually, Ghemor offers to help her escape the harsher interrogation she will undoubtably suffer at the hands of the Order, revealing himself as a member of Cardassia's underground dissident movement. In a moment of insight, Kira realizes that the entire affair — her abduction, her 'Cardassian' identity, her supposedly blocked memories — were all staged in an attempt to reveal Ghemor as a dissident.
Odo, Garak, and Commander Sisko arrive in time to prevent the Order from taking Kira and Ghemor away for punishment. A firefight breaks out and Entek is shot by Garak (who wryly points out: "Pity. I rather liked him.") Back at Deep Space Nine, tests reveal that Kira is definitely Bajoran. Ghemor understands that she is not really Iliana, but declares that he will never stop hoping that Iliana is alive and will return to him.