Sisko has learned from Odo that a Changeling has taken Gowron's form, and is now in control of the Klingon empire. Sisko is then ordered by Starfleet Command to expose the Changeling. He decides to take Odo, O'Brien, and Worf with him on the mission. The difficulty with the mission is getting close enough to the imposter Gowron to expose him as a Changeling - the only way they can get close enough is to pose as Klingons. Julian Bashir is called upon to surgically alter them to that end (even Worf is altered so that his cranial ridges are different, to keep him from being recognized). Sisko is also given four metal spheres which, when activated, will emit radiation which will force any nearby Changeling to revert to its natural gelatinous state.
In order to get to the heavily guarded Ty'Gokor station, Sisko calls upon Gul Dukat. Previously, Dukat had captured a Klingon Bird of Prey, which Sisko hopes can get them to Ty'Gokor undetected. Onboard the Bird of Prey, Worf trains the humans on how to behave like Klingons. Dukat also lends assistance by creating Klingon identities for each of the four. He adds them to a list of candidates that will receive the Order of the Bat'leth, which is awarded by Gowron himself. This gives them the opportunity to get close enough to set up and use their emitters. After arriving at Ty'Gokor, Dukat transports them to the surface and leaves them to fend for themselves. If they are successful, the war will end and they will be able to leave Klingon space. If they fail, it will not matter as they will be executed as spies.
The four arrive at the Hall of Warriors, where the ceremony has already begun, and try to blend in as best as they can. Soon General Martok, second in command to Gowron, arrives, indicating that Gowron will be there soon. The four then scramble to set up their receivers, not without some difficulty. O'Brien then encounters a problem, Martok seems to recognize him. But he is able to convince Martok that they fought in a battle together. Odo is then bumped by a drunk Klingon causing him to drop the emitter, but with Worf's help he is able to convince the Klingon that it is a toy. Odo then attempts to set his emitter up once more, but this time there is another Klingon in his way. Odo then, acting every bit a Klingon throws him from his spot and finally manages to set up the emitter. Sisko is then called out to receive his award, after receiving the award, he attempts to activate the emitters. But he is knocked to the floor by Martok, who has finally recognized them. He has them thrown in a security cell.
Once they have privacy, Martok confides to Sisko that he too believes that Gowron is an imposter. He says that Gowron ordered that the emitters be destroyed, but still agrees to help, saying that only way to expose Gowron is to kill him. Martok then releases Sisko and his group and leads them back to the Hall of Warriors, but keeps Odo outside, saying he does not trust him. Worf proceeds to attack Gowron who insists on fighting him one on one, just as a real Klingon would. Martok wonders why Sisko does not shoot Gowron outright. Odo realizes that Gowron, in choosing to stand to fight Worf, is showing Klingon honor, and that it is Martok who is the impostor. Odo reveals the faux Martok to the crowd, and the Klingons open fire. The Changeling is quickly destroyed.
Gowron then realizes that Odo was led to believe he was the Changeling, this way he would be killed by the Federation allowing the fake Martok and the Founders to gain control of the Empire. Gowron also expresses his doubt that the war will end since Klingons do not turn from battle, but he does agree to a cease fire, and has Sisko and his men returned safely back to DS9