After Kirk fails to convince the Halkan Council to allow the Federation to mine dilithium crystals on their planet, the landing party (Kirk, McCoy, Scotty, and Uhura) returns to the Enterprise. Interference from an ion storm, however, causes them to be transported into a parallel universe and a mirror image Enterprise.
Now aboard the I.S.S. Enterprise (Imperial Starship Enterprise), the landing party discovers crew members who are mirror images of themselves and belong to an evil Federation known as the Empire. Their first experience is the torture of transporter operator Mr. Kyle with an agonizer for his alleged failure to beam the landing party up quickly enough. Immediately, Kirk realizes that a mirror image landing party (including an anti-Kirk) must have been beamed aboard the real U.S.S. Enterprise.
Kirk, Uhura, McCoy, and Scotty impersonate their mirror image counterparts while finding a way to return to their universe. Kirk learns that he has been ordered to annihilate the the Halkans, but piques Spock's curiosity by ordering the Enterprise to hold its fire for 12 hours. Kirk then survives an assassination attempt by Chekov when one of his party defects, and then subjects Chekov to the agony booth. Kirk also uses the computer to determine that he succeeded to command by assassinating Christopher Pike and was responsible for the death of 9000 colonists on Vega.
While Scotty is adjusting the transporter to return them back to the correct universe, Kirk meets Marlena, the ``Captain's Woman.'' Meanwhile, anti-Spock has received a directive to kill Kirk if he does not carry out his orders by destroying the Halkans on the Enterprise's next orbit. Marlena shows Kirk the Tantalus Field, which he recovered from a lost civilization and has been using to eliminate his enemies.
Another assassination attempt, this time by Sulu, is crushed when Marlena uses the Tantalus Field on Sulu's co-conspirators. Kirk stalls Spock by knocking him unconscious, and Uhura, Kirk, and Scott head for the transporter room while McCoy stays behind to make sure that anti-Spock is all right. Anti-Spock the comes out of his self-induced trance and mind melds with McCoy. Discovering that a switch has occurred, anti-Spock then assists Kirk in returning his landing party to their own universe so that the Empire landing party may return to its.
When Kirk and the party return, they find that their Empire counterparts were immediately recognized and put in detention. The Enterprise's crew attributes this to the fact that it is easier for logical men to appear barbarous than for barbarous men to appear civilized.