With war declared between the Klingon Empire and the Federation, Starfleet summons Captain Benjamin Sisko and Lt. Commander Jadzia Dax back to Earth to discuss Odo's dire belief that Gowron, the chancellor of the high council, has been replaced by a Changeling and is pressing forth the war.
Starfleet equips Sisko with modified polaron emitters with a mission to infiltrate Klingon military headquarters on Ty'Gokor to expose Gowron to polaron radiation; if he is a changeling, exposure to the radiation will make it impossible for him to retain his humanoid shape.
Surgically altered to look like Klingons, Sisko, Odo, Chief O'Brien and Lt. Commander Worf set course for Ty'Gokor in Gul Dukat's Bird-of-Prey. En route, however, Dukat's holographic filter malfunctions just as a Klingon Bird-of-Prey confronts them and demands visual contact. Worf suggests that he talk the other captain down, but Dukat does not trust Worf and abruptly fires his ship's disruptors at the other Bird-of-Prey, totally destroying it. With the filter off-line, Dukat has no choice but to leave the DS9 officers on Ty'Gokor and leave Klingon space. When Sisko protests, Dukat assures him that if he is successful, the war will be over and they won't need his ship to return.
Beaming into Ty'Gokor, the Order of the Bat'leth ceremony is underway in the Hall of Warriors, with hundreds of drunken Klingons intending to celebrate all night in anticipation of Gowron's arrival. Worf informs the crew that the celebrations are an endurance test, and that only those who can drink and celebrate for the whole night and remain conscious the following morning will be inducted into the Order. Waiting until morning to set up their emitters, the DS9 officers begrudgingly partake in the festivities in order to blend in. During the course of the night, Sisko demonstrates his combat skills on several of the Klingons, and takes the opportunity to assault a Klingon who had killed one of Sisko's former Starfleet Academy classmates (though Sisko uses the excuse that the Klingon was in the way of the barrels of blood wine). By the following morning, Sisko and his crew are still coherent, thanks to an alcohol inhibitor provided by Bashir. When Martok arrives, Sisko fears he may recognize them. Although Martok feels he recognizes O'Brien, the Chief gets away with it by claiming to have fought at Mempa along with Martok, which satisfies his curiosity.
As Gowron arrives, the DS9 crew set-up their emitters and prepare to activate them when Sisko is summoned by Gowron to join the Order of the Bat'leth. Sisko accepts the commendation. As he turns, he begins to activate the emitters, when he is attacked from behind by Martok, who now recognizes him.
Thrown into a holding cell, Sisko presses Martok, as he believes that Martok thinks that Gowron is a Changeling, as well. Martok cannot hide his feelings and agrees to help the DS9 officers kill Gowron, though strangely refuses the notion of challenging Gowron to a duel himself. As they fight their way back into the Hall of Warriors, Worf challenges Gowron to a fight to the death, while Martok holds Odo at gunpoint, unwilling to trust a former Changeling. When Martok wonders why Sisko doesn't simply shoot Gowron, Odo realizes that a true Klingon wouldn't cowardly shoot someone and deduces that Gowron isn't the Changeling, but Martok is.
Worf gains the upper hand on Gowron and shatters his Bat'leth, and just as he goes to make the killing blow, Odo and Martok brawl their way into the hall. Knocked to the ground, Odo exclaims "Martok is the Changeling!" Exposed, the Martok changeling begins to choke Odo with a tendril of his shapeshifting body, but, he is blasted by Sisko's disruptor. As the other Klingons see Martok for what he really is, they begin firing as well, resulting in the Changeling's death.
With the dust settled, Gowron realizes that the Founders had led Odo to believe that he was a Changeling, hoping that Starfleet would try to eliminate him. With Gowron out of the picture, the Martok Changeling would be able to rule the Klingon Empire, pressing for war with the Federation and the Cardassian Union, destabilizing the Alpha Quadrant and leaving it wide open for a Dominion invasion. Sisko informs him that the best way to strike a blow against the Founders would be to end the war between the Federation and the Klingon Empire, but Gowron informs Sisko he can't if the Federation refuses to allow the Empire to annex Archanis. Sisko believes that the Federation won't agree, but, believes there's room for negotiation. Satisfied, Gowron decides to declare a cease fire and arranges for the DS9 officers to return home.