After experiencing operational difficulties while traveling through the Wormhole, Major Kira and Dr. Bashir find themselves in an alternate universe where the station is populated by exact doubles of Garak and Odo, and is run by Kira's counterpart, who is referred to as 'Intendant'. In this universe, they have no knowledge of the wormhole, and humans have no rights whatsoever. Because of this, Bashir is sentenced to manual labor, working under the sadistic, human-hating alternate Odo. Later, the Intendant tells Kira about the last crossover, which occurred with Captain Kirk a century ago as seen in TOS episode "Mirror, Mirror". That incident led to the formation of a powerful alliance between the Klingon and Cardassian Empires in which Bajor is also a major player. The Intendant says that she cannot allow Kira and Bashir to live, but Kira convinces her counterpart to spare them and let her try to find a way back.
Kira steals a moment with Bashir and tells him what she knows. Since a transporter accident caused the last crossover, Bashir thinks they might be able to escape using another one, and tries to talk O'Brien's counterpart into helping him. Unfortunately, the beaten, put-upon Terran has little interest in risking the wrath of his superiors. Meanwhile, Kira almost succeeds in securing help from this universe's Quark, but he is arrested by Garak – the Intendant's aide, and (unlike the normal universe's Garak) a Gul in the Cardassian military – for helping Terrans escape the station.
Kira then meets Sisko's Mirror Universe counterpart, who receives better treatment than the other Terrans because he runs missions for the brutal Klingon/Cardassian Alliance. Afterwards, the Intendant reassures Kira that she has nothing to fear, and suggests they should become closer. Later, Garak tells Kira that he intends to dispose of the Intendant, and that he will let Kira and Bashir escape if she pretends to be her double, then resign and allow Garak to take over. Garak then casually reveals Bashir will be killed if she does not comply.
Kira hurries to Bashir and tells him they must find a way back to the runabout and make their escape through the wormhole. She fills Sisko in on Garak's plan, hoping he will help out of loyalty to the Intendant, but he is unmoved. That night, Garak prepares to put his plan into effect at a lavish party thrown for Kira by her counterpart. Meanwhile, Bashir is able to take advantage of an accident at the ore-processing plant where he labors, killing Supervisor Odo and escaping.
News of Bashir's escape soon reaches the party, while Bashir manages to locate "Smiley" O'Brien, who decides to help this time. However, the two are caught and brought to the party to face the Intendant. Despite Kira's pleas, Bashir is sentenced to death. "Smiley" then makes an impassioned speech, telling the assembled crowd what Bashir has revealed about a universe where Terrans have respect and dignity. His words move Sisko, who turns on the Intendant and helps Kira and Bashir to escape. The two return to their universe, leaving Sisko and O'Brien's counterparts to fight for the rights of Terrans in their own world.