Admiral Ross at Starbase 375 uncovers a major reason for the Dominion's dominance — a sensor array monitoring all activity across five sectors. Sisko soon formulates a risky plan to disable it. Back on Terok Nor — the Cardassian name for Deep Space NineKira and her "resistance cell" of Jake, Rom and Odo work to foster ill will between the Cardassians and the Dominion. When Odo speaks out against her latest scheme, Kira begins to question his loyalty.

Later, Admiral Ross promotes Sisko, removing him from the Defiant. Dax, now in command of the ship, will run the mission without him. Meanwhile, Odo is surprised to encounter on the station the Female Shapeshifter who once took away his changeling abilities. She tells Odo that he has been forgiven for killing one of his people, and, playing on the pain of his unrequited love for Kira, persuades him to link physically and merge with her.

When Kira learns of this, she asks Odo not to link with the Female Shapeshifter again, which he promises. Later, Quark barges in on Kira's secret meeting with Jake, Rom and Odo. He learned that Damar, Gul Dukat's second-in-command, has figured out how to use the station's deflector array to deactivate Rom's self replicating minefield — the one thing that stands between the station and hordes of Jem'Hadar troops waiting on the other side of the wormhole.

Based on information Quark provided, Kira devises a plan to disable the deflector array. Odo will run a security diagnostic, giving Kira and Rom a five-minute window to sabotage the equipment before being detected. But the next morning, while Kira and Rom prepare for their mission. Odo again links with the Female Shapeshifter, ignoring his promise to Kira. When Kira goes to the Security Office, she finds it empty, and Odo doesn't respond to her calls.

Kira hurries to call Rom, but she's too late, and Rom is arrested. Furious, Kira barges into Odo's quarters and is shocked when he serenely admits that he did indeed rejoin the link. Suddenly, for the first time ever, Kira and Odo are on opposite sides, and she regards her longtime friend as an enemy. But all is not lost. Light years away, the Defiant returns to Starbase 375 intact, and Sisko wistfully witnesses the celebration of Dax's first successful mission.