The Enterprise responds to a distress call from a scientific research team exposed to radiation on Camus II. Kirk, Spock, and McCoy beam down and find that the head of the expedition, Dr. Janice Lester, is one of the survivors. Dr. Coleman, the expedition doctor, is the other. Spock detects life signs and he takes McCoy and Coleman to investigate while Kirk stays to keep Janice calm. She recovers consciousness and talks about how they were at Starfleet together but she left after a year. He admits it isn't fair but there's nothing they can do. He goes over to examine an alien mechanism and Janice triggers a remote that paralyzes him. She then goes over, activates the machine, and their minds are transferred into the others' bodies.
Janice (Janice-K) picks up Kirk-L and drops her unconscious body on the couch. Janice-K plans to take Kirk's place and prepares to strangle her with her scarf. She's interrupted when McCoy, Coleman, and Spock return. McCoy says that the party was exposed to celebium, not radiation. They're interrupted when Kirk-L moans and Coleman realizes that Janice-K has made the switch. Janice-K has them beamed up to the ship and talks to McCoy, saying "she" was involved with Janice. McCoy promises to do whatever he can.
Kirk-L starts to revive in Sickbay and Janice-L tells Coleman to make sure she never recovers consciousness. Janice-L deliberately sent her team where the celebium shielding was weak, and wants Coleman to finish off Kirk-L for her. "She" points out that Coleman is in just as deep. McCoy and Chapel come in and contend that there are no signs of internal radiation exposure. Coleman disagrees and Janice-K turns the case over to Coleman over McCoy's objections. Kirk-L starts to recover consciousness and remember what happens but then passes out.
On the bridge, Janice-K orders them to set course for the Benecia Colony, which is closer. Spock contends that the colony's medical facilities are primitive and they should proceed to Starbase 2. Janice-K insists on holding to her order and starts snapping at Spock and the other bridge crew when reminded "he" has to notify Starfleet. McCoy then confronts Janice-K about Coleman's documented medical and administrative incompetence. When Janice-K standards by "her" orders, McCoy orders a complete physical and psychological check based on emotional irregularities. Janice-K accuses McCoy of trying to get revenge for the orders but has no choice but to give in under Starfleet regulations.
Kirk-L wakes up in Sickbay and Coleman comes in and pretends Kirk-L is Janice. Chapel comes in and Coleman claims Janice has been showing signs of instability now increased due to the radiation. Kirk-L sees "herself" in the mirror and starts to remember what happened. Confined to bed, Kirk-L tries to pass herself off as stable and asks Chapel if "she" can see McCoy or Spock. After getting a glass of juice and being left alone, "she" breaks the glass and cuts through her bonds.
McCoy and Spock are considering what to do about the increasingly erratic captain when Janice-K arrives for "his" examination. Kirk-L runs in and Janice-K quickly stuns her before she can say much. Spock goes to see Kirk-L with a guard supervising, and "she" suggests he mind meld. Convinced, Spock notes his belief isn't acceptable evidence and takes her to see McCoy, knocking out the guard when he tries to stop them. The guard sends out an alert while McCoy determines that "Kirk" checks out physically and mentally. They receive the security alert and arrive to take Spock into custody, and Janice-K orders a court martial.
At the court martial, Scotty conducts the questioning and notes they need evidence. Spock asks that they bring "Janice" in to testify and Janice-K has no choice but to yield. While she's brought in, Janice-K has McCoy testify as to the results of his tests. Coleman brings Kirk-L in but Janice-K orders him out. Janice-K then mockingly interrogates Kirk-L, who stands by "her" story. Spock notes that the question is whether the crew accepts that life-entity transfer is possible. Janice-K notes that he will take command and offers to forgive him, but Spock refuses to drop his charge. Janice-K insists that Spock's statements condemn him as a mutineer and calls an immediate vote with no discussion.
Scotty and McCoy discuss the case outside and Scotty believes in Spock. He notes that if they vote against Spock's court martial, they'll need to mutiny. They return and discover Janice-K has recorded their conversation, and plays it back. Janice-K orders their immediate execution but Sulu and Chekov object. Janice-K sends them to their posts and orders the "conspirators" to be prepared for execution.
On the bridge, Chekov and Sulu refuse to cooperate or take orders and Janice-K becomes increasingly hysterical, and then starts to feel the transfer reverse itself. In the brig, Kirk-L feels the same thing and they conclude the transference can be broken. Janice-K goes to Coleman and asks him to kill Kirk-L to ensure the transference remains permanent, and notes he has no choice. Janice-K and Coleman go to the bridge to separate them, transferring Kirk-L first. Coleman tries to inject her with a hypo but the transference reverses entirely. Janice is furious and Coleman tries to console her. They let him tend to her while Kirk notes she could have been happy if only… if only…