Stardate not given: Kirk and his landing party (Uhura, McCoy, Scotty) are meeting with the Halkan Council to gain rights to their dilithium, but the pacifistic race is leery that the Federation will use them for hostile purposes. They postpone the meeting until the Council can meet as a magnetic storm hits the planet. Kirk calls for beam-up and they start to materialize on the platform, but then there's an energy surge and they dematerialize then rematerialize… to find themselves on a different Enterprise… where Spock has a beard and they're all wearing more barbaric uniforms. When the "new" Spock asks if they should stick with standard procedure, Kirk covers and agrees… and Spock orders a phaser barrage of a Halkan city. He then sues a handheld agonizer device to torture the transporter operator Kyle for failure.
Kyle reports another problem due to the storm and Kirk says they're feeling abnormal effects and has McCoy take them to Sickbay. They realize they were in their own transporter chamber briefly before appearing here… some kind of parallel universe. They quickly realize that there was an exchange and their counterparts arrived in "their" universe. Kirk has Scotty short out the main phaser couplings using the storm as cover and then work out the technology to reverse the transport. Uhura goes to the bridge to get the command transmissions and finds a facially-scarred Sulu as the head of security. He flirts with her but she turns him down cold. Kirk arrives before he can get violent and Uhura reveals he has no choice but to attack the Halkans.
Kirk stalls as Spock arrives on the bridge and demands to know what's going on. Kirk finally calls off the attack and talks with the head of the Halkan Council, Tharn. Tharn refuses to give up the crystals and Kirk gives him 12 hours to comply. Spock notes his actions are unprecedented and will report his actions. Kirk calls a meeting with the landing party and Chekov leaves the bridge with him. When they arrive on Deck 5, three men grab Kirk and Chekov prepares to kill him to advance in rank.
One of the men, Farrell, turns against Chekov and disintegrates one of the others with a phaser while Kirk beats up on the others, who Farrell then kills. Kirk's personal guard arrives to haul away Chekov and Kirk slugs the greedy Farrell.
Back in his quarters with the landing party, Kirk has the computer work out that the transport can be reversed. Scotty takes the data and prepares to tap into the warp engines, but will need McCoy to help him. Kirk reviews his personal record with his use of assassination and slaughter. Scotty warns that the alteration will show up on Sulu's security board and Kirk says he'll have Uhura provide a distraction.
Back in the other universe, Spock has the mirror-Kirk and the others locked up despite the fact that Kirk offers him a bribe.
Kirk and mirror-Spock look on as Chekov is tortured in an agony booth. They leave and Spock questions Kirk's orders concerning the Halkans, expressing regret that Kirk's "aberrations" may jeopardize his position. Kirk heads back to his quarters after they exchange threads.
McCoy drugs a security guard so he and Scotty can get to the warp conduits. Kirk returns to his quarters to find a woman waiting for him--Lt. Marlene Moreau, the "Captain's woman." She wonders if he's aiming for a council seat and kisses him. They're interrupted when Spock calls to warn that he's had a private communication from the Empire ordering him to give Kirk until planet's dawn in three hours and then kill Kirk and eliminate the Halkans.
Moreau wonders if Kirk will kill Spock and asks him if she can activate the Tantalus Field. She opens a wall panel to reveal a monitor that can view Spock and Moreau threatens to use it to vaporize Spock, but Kirk tells her not to, much to her surprise. Kirk assures her she'll have a place at his side. When she leaves the room for a moment, Kirk warns Scotty of the new deadline and Scotty warns that due to the altered field density, they only have a narrow window to transport back or they can't return for a century.
Sulu detects the computer activity and contacts Spock, and Spock notes he doesn't wish to be captain… but his operatives will avenge his death if Sulu kills him.
Moreau thinks Kirk is rejecting her and when she notices Kirk's (relative) compassion toward her, senses something is wrong. He leaves to let Uhura know the situation, leaving Moreau to ponder what's going on.
Kirk heads for the bridge and notifies Uhura that Scotty's signal is coming through. She starts flirting with Sulu to distract him from his security board, then changes her mind again and draws a knife when he comes at her.
Down in the transporter room, Kirk is working at the controls when mirror-Spock arrives and holds him at gunpoint, then demands answers. Spock decides to go to McCoy and interrogate him with Kirk as his prisoner. He finds the entire landing party in sickbay but Kirk gets the drop on him. A fight breaks out and Spock tosses them around until Uhura gives Kirk a jar to hit him over the head with. Spock is dying and they only have 15 minutes left, but McCoy insists on treating him. Kirk agrees… while Moreau monitors them on the Tantalus Field. Sulu arrives in sickbay with his men and announces his plan to kill them all so he can become captain.
Moreau disintegrates Sulu's three crewmen but leaves the security chief for Kirk. Kirk readily disposes of him but time is running out. McCoy tells them to go on ahead and he'll meet them. They leave, McCoy revives Spock, and the first officer uses the mind meld to interrogate him.
The others arrive in the transporter room to find Moreau there. She asks him to go along but the power is balanced for four. When he refuses, she draws a phaser on Kirk but Uhura disarms her. Power is cut and Scotty can get the auxiliary power, but someone will have to operate the controls manually. Scotty volunteers but Kirk overrides him. Spock arrives and says he temporarily cut out the power until he arrived. He restores power and Kirk asks him how long the Empire has. When Spock notes it will eventually fall apart, Kirk points out it's illogical to support it. Kirk tells him about the Tantalus Field and Spock says he'll consider it.
They beam back onto their Enterprise. Later on the bridge Kirk meets his new lieutenant… Marlene Moreau.