Captain Kirk, Dr. McCoy, Scotty, and Uhura unintentionally end up on the ISS Enterprise, a different model from the USS Enterprise, due to an ion storm. However, Kirk can recognize mirror Spock, despite his facial hair and a gun on his hip. Furthermore, the ship belongs to an empire instead of the Federation. After asking about the mission, Spock orders the bridge staff to prepare a phaser attack on the Halkans for their refusal to help. He then uses an "agonizer" to punish Transporter Chief Kyle for a mistake.

Kirk tells the away team to go to Sickbay to figure out what happened to them. He guesses that the ion storm broke down a barrier between two universes, resulting in the two teams swapping galaxies. To keep up the ruse, they decide to act like their counterparts until they can get back. Uhura discovers that Starfleet has commanded the Halkans to be obliterated if the Empire's requirement for dilithium is not satisfied. Kirk gives them a twelve-hour delay to answer, which Spock reports to Starfleet. Later, Kirk heads to his room and is almost murdered by Chekov and his associates, one of whom ends up saving Kirk's life. Kirk's bodyguards take Chekov to the "Agony Booth" for discipline.

When Scott and McCoy join Kirk in his quarters, the computer verifies Kirk's presumptions. It supplies a method to re-enact the transporter mishap and restore them to their own universe. Kirk also uncovers that in this world, his twin had seized control of the ISS Enterprise by killing Captain Christopher Pike and had committed numerous wrongdoings since then. Meanwhile, on board the USS Enterprise, Spock puts their mirror-universe counterparts in custody, but he has yet to decide how to send them back home.

Scott and McCoy begin work on the engines and transporter on the ISS Enterprise. Spock warns Kirk that he cannot support Kirk's aberrant behavior despite their relationship. Kirk defies the warning and releases Chekov from the Agony Booth. When Kirk returns to his quarters, he finds Marlena, the "captain's woman." Spock interrupts them and informs Kirk that he has been ordered to kill him if he does not carry out his mission. Afterward, he will take command of the ISS Enterprise. He reassures Spock and Marlena that she is still the captain woman and the "captain's woman."

Spock employs the computer to investigate the "secretive research" happening in Engineering. Spock blocks Kirk's path in the transporter room and directs him at gunpoint to Sickbay, where Scott, McCoy, and Uhura are already waiting. When they arrive at Sickbay, Kirk knocks Spock out as Sulu appears with three security guards. Marlena aids Kirk by using the Tantalus Field to disintegrate Sulu's allies. As Uhura, Kirk, and Scott move toward the transporter room, Spock regains consciousness and forces McCoy into a Vulcan mind meld. Spock figures out the situation and resolves to get his own commander back.

Spock arrives in the Transporter room and announces he will operate the controls. Spock promises to consider what he and Kirk discussed about the fall of their Empire as he transports them out.

Kirk, McCoy, Scott, and Uhura transport themselves back to the world of the Federation.