Eager to aid Damar's rebel movement on his homeworld against the Dominion, Sisko orders Kira to put her antipathy for the Cardassian aside and train his staff in resistance tactics. Bashir asks Odo to assist in his medical project by donating the Changeling-equivalent of a skin sample. On Bajor, Kai Winn studies the forbidden text of the Kosst Amojan to learn how to release the evil Pah-wraiths. Hoping to ease Cardassian sentiment against the Bajoran Kira, Sisko gives her a Starfleet commission and uniform.
Damar and his Cardassian assistant Gul Rusot await Kira's arrival, realizing she has the skills they need to prevail. General Martok prepares to be inducted into the Klingon Order of Kahless by Chancellor Gowron. Bashir and Ezri meet, but he incorrectly assumes she loves Worf. Studying Odo's sample leads Bashir to conclude that Odo is infected with the deadly Founders' disease.
Although shaken by Bashir's findings, Odo insists he and Kira proceed with the Cardassian mission. In Kai Winn's office, Dukat is blinded when he sneaks a look at the Kosst Amojan. Hoping to find a cure, Bashir unsuccessfully tries to get Odo's medical records from Starfleet Medical. Following Martok's induction, Gowron betrays him by overtaking his command of the Klingon forces.
At the rebel outpost, Damar's staff bristles at some of Odo and Kira's strategic advice. With Sisko's help, Bashir secures Odo's medical file, only to realize it's fake. To their horror, O'Brien and Bashir theorize Odo's records were altered by Section 31, an insurrectionary group within Starfleet, which doesn't want Bashir to cure the disease. Later, one of Damar's officers tries to provoke Kira by reminding her of Odo's past "collaboration" with the enemy, while privately, Odo notes the first signs of the deadly disease taking hold.
Kai Winn puts the blind Dukat on the streets as punishment for defying the Pah-wraiths. Martok is shocked when Gowron, hoping to restore the glory of the Klingon Empire, selfishly proposes sending far-outnumbered Klingon troops into Domionion territory. Bashir suspects Section 31 created the virus and infected Odo as a carrier in a genocidal plot. With O'Brien's help, Bashir vows to discover the cure he feels certain Section 31 has in its possession.