Plot summary
The Dominion has deployed a new weapon that can disable starships with one shot; only Klingon ships can be made resistant to it as yet, and so the entire defense of the Alpha Quadrant is in the Klingons' hands for the time being. Klingon Chancellor Gowron visits DS9 to honor General Martok, the commander of the Klingon fleet, by inducting him into the Order of Kahless; but after the ceremony he announces he is assuming command of the fleet himself. He outlines his plan for a new offensive into Dominion territory in order to seize glory for the Klingon Empire, ignoring Martok's objections that they are badly outnumbered by Dominion forces and are overextended already merely defending the border.
To aid Damar's revolt against the Dominion, Captain Benjamin Sisko sends Kira, a veteran of the Bajoran resistance against Cardassian occupation, to train the Cardassians in guerrilla warfare strategies and tactics; she is accompanied by Odo and by exiled Cardassian spy Elim Garak. Anticipating the Cardassians' objections to being advised by a Bajoran former terrorist, Sisko has Kira given a Starfleet commission to lend her more authority. When she arrives at Damar's camp, his men object to her presence—especially when she tells them they must be willing to kill fellow Cardassians if they collaborate with the Dominion—but Damar is willing to take her advice seriously.
Bashir, examining a tissue sample from Odo, discovers that Odo is infected with the same disease plaguing the Founders. Attempting to develop a treatment, Bashir requests a copy of Odo's full medical records from Starfleet. Starfleet bureaucrats stonewall his request, claiming that the records are classified and questioning Bashir's loyalty for trying to cure a disease that primarily threatens the Federation's enemies. When Sisko compels Starfleet to send Bashir a file, he discovers it is a fake. Extrapolating the history of the infection in Odo's system, Bashir conjectures that Section 31, Starfleet's secretive black ops division, deliberately infected Odo with the virus so that he would transmit it to the Founders.
Kai Winn is studying the forbidden Text of the Kosst Amojan to learn how to release the Pah-wraiths from their confinement. Dukat sneaks a look at the book and the Pah-wraiths punish him by blinding him. Winn throws Dukat out to live as a blind beggar, telling him he can return when his sight is restored.
Credits
Adapted from Wikipedia contributors, When It Rains.... Paragraphs and formatting adjusted; illustrations, reference markers, block quotations and non-story material omitted.