Sisko is meeting with Odo and Quark in his office, and is listening to Odo's report about Quark's latest misdeeds. It seems that Quark had a number of Cardassian voles hidden in his storeroom. Quark tries to explain that vole infestations are not an uncommon occurrence. Odo counters that Quark and Morn were painting numbers on the vole's backs. When Sisko accuses Quark of preparing to stage a vole fight, Quark feigns innocence, and says that he has no idea that Morn was planning to use the voles for such a purpose. Sisko orders the voles confiscated and removed from the station, Quark says that Morn will be heartbroken because the voles were like pets. Sisko responds that he'll get Morn some goldfish.
As he leaves from the security meeting, he is abducted by a double of Miles O'Brien, who takes him to the Mirror Universe that Kira Nerys and Julian Bashir visited the year before. This O'Brien explains that Sisko's counterpart, the leader of the Terran rebellion against the Klingon/Cardassian Alliance, has been killed. O'Brien wants Sisko to pose as his dead counterpart and convince a Terran scientist with the Alliance to join the rebels. That scientist is Jennifer Sisko, the Mirror counterpart of Sisko's late wife. Since she is building a sensor device that will betray the secret location of the rebels in the Badlands, Sisko must convince her to join them before she completes her work or the rebels will have to kill her. Unwilling to watch Jennifer die again, Sisko agrees to intervene. He meets the rebel counterparts of Bashir and Rom, and also Jadzia Dax, who is Sisko's mistress in this universe. The rebel group in the Mirror Universe includes the counterpart of the Vulcan Tuvok, who in the original timeline is currently stranded with the rest of the crew of Voyager in the Delta Quadrant.
Terok Nor, the Mirror Deep Space Nine, is ruled by Intendant Kira for the Alliance. She tells Jennifer that the bloodshed against the Terrans will end once her device is completed. But later, Kira tortures Terran slaves in the ore processing center with the help of Garak, her chief aide. Then, Kira discovers that Sisko is still alive.
With communicators hidden under their skin, Sisko and O'Brien take a rebel ship to Terok Nor. They are immediately captured and taken to Kira, who sends O'Brien to ore processing with the slaves and takes Sisko to her quarters. Later, Sisko meets Jennifer, who despises him, and without revealing his true identity, apologizes for his past treatment of her, then says that he has come to rescue her.
Sisko tries to convince Jennifer that the Alliance is her real enemy, and plans to kill the rebels once they are found. Sensing he may be winning her confidence, Sisko signals O'Brien. In ore processing, O'Brien receives the signal and causes a malfunction that allows him and the Terrans to escape. Meanwhile, Jennifer agrees to leave with Sisko, they meet O'Brien, then head for a waiting ship.
Before they can escape, however, they are cornered by Kira and her troops. While Kira waits for Sisko to surrender, he slips away and herds his entire group into the ore processing center, where they seal themselves within. When Kira, Garak, and her soldiers finally force their way in, Sisko calmly tells her that he has activated the station's self-destruct sequence, which only he can stop. Kira reluctantly agrees to let Sisko, Jennifer, O'Brien, and the Terrans go free in order to halt the imminent destruction. Sisko and the others return to the rebel encampment, where Jennifer admits to realizing that he's not really her husband. She kisses him goodbye, and Sisko returns to his universe just a bit sadder.