The year is 2375. Having just lost the Second Battle of Chin'toka, Starfleet's Miles O'Brien has determined that the only vessel immune to the Breen energy dampening weapon was the Klingon Bird-of-Prey Ki'tang. The chief engineer of the Ki'tang had adjusted the tritium intermix of the vessel's warp core, so the same adjustment is made to all Klingon vessels in the fleet to protect them from the Breen; unfortunately, this "fix" works on neither Federation nor Romulan ships. O'Brien forwards his findings to both Starfleet Engineering and the Romulan Ministry of Science for more in-depth analysis.
General Martok and Captain Sisko plan to use the Klingon fleet as a diversion, to occupy the attention of the Dominion and the Breen. In the meantime, Starfleet will continue searching for an answer to the Breen weapon, while hoping the Cardassian uprising, led by Legate Damar, grows in strength, to further sap Dominion resources. To help Damar in his new role as leader of an underground movement, Sisko and Admiral Ross agree to send Kira to his aid; with her years of experience in (ironically) the Bajoran Resistance, she has a lot to teach Damar in how to wage a guerrilla campaign. Putting aside her personal feelings, she agrees, and will also bring along Garak, whose experience in the Obsidian Order promises to pay dividends, too.
On Bajor, Kai Winn feigns concern over the disappearance of Solbor, whom she recently murdered. Dukat, his true identity revealed to the Kai, continues to encourage the Kai on her path toward unleashing the Pah-wraith from the fire caves. As she continues reading the sacred Book of the Kosst Amojan, Dukat offers to help her, but she refuses, saying the book's words are for her eyes only. In the middle of the night, however, Dukat sneaks into the Kai's study, unlocking the book, and reading its secret text. Suddenly, a beam of red energy (resembling a Pah-wraith) leaps from the pages of the book into Dukat's eyes, blinding him.
In order to give Kira some sense of "authority" over her Cardassian comrades (and students), Sisko gives her a battlefield commission of Starfleet Commander. Later, after Kira dons her new Starfleet uniform, Odo morphs his attire to more closely resemble how he appeared as the Terok Nor's security chief (when DS9 was under Cardassian control). Garak continues to warn Kira that she, a Bajoran, should never trust the Cardassians she will be working with and training.
The crew of DS9 greet Klingon chancellor Gowron, visiting from Qo'noS in order to induct Martok into the Order of Kahless. Gowron, who puts the past to rest with Worf, arrives with a barrel of bloodwine to be shared by old friends. Doctor Bashir, while trying to speak personally with Ezri Dax, gets the wrong idea that she and Worf are a romantically-involved couple. As she tries to explain that they are only friends, Julian's attention is diverted to a disaster in his lab: he discovers that Odo is infected with the same virus killing the Changelings of the Great Link.
After Gowron awards Martok the Star of Kahless, Gowron informs everyone that he (Gowron) would be immediately taking command of the war effort; thus, a day of honor for Martok has become bittersweet, as he loses his command. Feeling betrayed, Martok nevertheless pledges his allegiance to the Empire, regardless of its current direction.
While Starfleet is stonewalling Dr. Bashir about Odo's Starfleet medical records, they begin to question his loyalties, since he is trying to cure a disease afflicting the Founders of Starfleet's greatest enemy, the Dominion. When he realizes later that he has been provided with phony data, rather than real medical data, regarding Odo, Julian begins to wonder if Section 31 is somehow involved in a cover-up.
Damar welcomes Kira to the headquarters of the Cardassian Liberation Front. While he is genuinely grateful for Kira's assistance, Gul Rusot still harbors long-standing ill will toward her, and makes no secret of it. Nevertheless, Kira and Garak begin educating Damar's group in the art of resistance. When Damar initially balks on supporting an attack plan against a Dominion base guarded by fellow Cardassians, Kira convinces him that those Cardassians are merely collaborators. Trying to provoke Kira, Rusot questions Odo about his past association with Cardassians on Terok Nor, insinuating that Odo was himself a collaborator. Kira jumps to Odo's defense, but the cooler heads of Garak and Odo prevail (for now). Odo, however, begins experiencing his first signs of the sickness, but keeps it a secret from everyone else, even Kira.
On Bajor, the Kai informs a blind Dukat that doctors can find nothing wrong with his eyes; his condition is obviously a punishment from the Pah-wraiths, who took away his vision for reading the sacred texts. By now, the Kai has discerned Dukat's true loyalties, which don't lie with her, so she summons a deputy to escort Dukat out into the street, helpless; she refers to it as a "lesson in humility for a blind beggar". Screaming as he is brusquely shown the door, Dukat is told by the Kai to return when he has recovered his vision (i.e., when he has once again found favor with the Pah-wraiths). Now alone with the sacred book, the Kai devotes her full attention to studying it.
Gowron astonishes Worf and Martok by suggesting an aggressive course of action against the Dominion, rather than just holding the line until the Federation and Romulan vessels are up to speed. Citing the element of surprise, and citing the glory to be had as saviors of the Alpha Quadrant, Gowron insists that his risky strategy is not up for debate, and will commence forthwith. Meanwhile, in sickbay, Quark brings some coffee to a weary Bashir and O'Brien, as his way of helping find a cure for Odo. While they discuss possible Starfleet cover-ups, Doctor Bashir finally discovers the actual conspiracy: that Odo was infected with the sickness by Starfleet, as a Section 31 plot of genocide against the Changeling race, including Odo.