Kira goes to train Damar's Cardassian rebels, Gowron takes over the Klingon fleet, and Bashir learns Odo carries the Founders' disease.
The Dominion has a new Breen weapon that disables ships, and only Klingon vessels can yet be protected, leaving the Alpha Quadrant's defense in their hands. Gowron visits to honor Martok, then takes command of the fleet himself and plans an offensive Martok warns is reckless. Sisko sends Kira, with Odo and Garak, to teach Damar's new Cardassian rebels guerrilla tactics, giving her a Starfleet commission to ease Cardassian resentment of a former Bajoran terrorist.
Bashir discovers that Odo is infected with the disease killing the Founders, and Starfleet stonewalls his request for medical records, eventually sending a forgery. Bashir concludes that Section 31 deliberately infected Odo to pass the disease to the Founders. Meanwhile Dukat reads the forbidden Kosst Amojan and is blinded by the Pah-wraiths, and Kai Winn casts him out. The episode opens the final arc, bringing together several of its central threads.