When the Enterprise stops by to pick up scientific staff Linke and Ozaba from the planet Menarian 2 (which is in orbit around a star which is about to supernova), Kirk, Bones, and Spock discover the station has been abandoned for three months. Meanwhile, Scott reports a massive solar flare measuring 3.51 on the ``Ritter'' scale. Kirk informs Scott to move the Enterprise to a safe distance until the flare passes, putting it out of communication range for 74.1 solar hours.
The landing party reviews the record tapes to see what has become of the scientific staff. It the tape, a high pitched whine begins, and Linke and Ozaba are whisked away one at a time while attempting to cover their ears. After reviewing the tape, Kirk and company are subjected to the same high-pitched whine, and are transported underground to the chambers of the Vions, 121.32 m below the surface.
Here, they discover a timid, mute, woman. McCoy starts to approach, but Kirk holds him back. When McCoy protests that she seems harmless enough, Spock reminds him that ``The sand bats of Maynard 4 appear to be inanimate rock crystals, doctor, before they attack.'' Kirk wonders how he will communicate with the woman unless she is a telepath. However, Spock notes that this is unlikely, since 98% of known telepathic species send as well as receive thoughts. McCoy dubs the woman Gem.
While Kirk is trying to question Gem, two Vions appear. When Kirk tries to secure freedom for the landing party, the Vions trap McCoy, Spock, and Kirk in a force field which draws energy from their bodies. The Vions then vanish, releasing the landing party. Gem then touches Kirk's forehead, transfers the wound there to her own head, and heals it, revealing herself to be an empath.
Spock reports that his tricorder now reveals a collection of machinery which did not appear to be there before. When they go to investigate, they discover Linke and Ozaba encased in plastic cylinders. In addition, there are three empty cylinders, labelled ``Subject McCoy,'' ``Subject Kirk,'' and ``Subject Spock.'' One of the Vions then reappears, but Kirk distracts him while Spock nerve pinches him. However, the Vion is only pretending to have fainted, and the landing party does exactly what the Vions intended when they head up to the planet surface.
On the surface, the Vions create an illusion that Scotty is on the surface with a search party. This distracts McCoy and Spock while the Vions study Kirk and offer to let the others go if Kirk offers himself as a ``specimen.'' The Vions torture Kirk without apparent reason. They then let him go, but Kirk finds that McCoy and Spock are still subterranean prisoners. Gem cures Kirk's injuries (including a case of the bends), but then faints from the strain.
Although Kirk does not yet realize it, it turns out that the Vions are testing the empath Gem to see if she will sacrifice herself by saving members of the Enterprise's crew. The Vions have the ability to save the inhabitants of only one out of several planets doomed to destruction, and wish to see if Gem's planet is worth saving. The Vions require another test, and give Kirk the choice of selecting McCoy (who will likely be killed) or Spock (who will likely suffer permanent brain damage). While Bones is bemoaning being trapped underground, he reports ``I'm a doctor, not a coal miner.'' Bones tranquilizes Kirk to give him rest (and to prevent him from picking Spock), but Spock points out that he is now in command and will select himself. McCoy then sneaks up on Spock and tranquilizes him as well, leaving only himself when the Vions come for a volunteer.
When Spock awakens, he adjusts a control device he has obtained from one of the Vions to operate using his own brainwaves, and transports Kirk, himself, and Gem to the torture chamber. They find McCoy is tied up and nearly dead, with almost no pulse, internal injuries, bleeding in the chest and abdomen, hemorrhage in the spleen and liver, and 70% kidney failure. Gem attempts to save McCoy, but stops before she kills herself in the process. She tries again, but McCoy pushes her away.
The Vions appear and watch the spectacle, locking Spock and Kirk inside force fields. Spock meanwhile manages to release himself from the force field by suppressing all emotion. He takes one of the control devices away fro the Vions, but is unable to use it to cure McCoy. Kirk secures freedom and a promise to save Gem's planet when he convinces the Vions that Gem has already earned her planet's survival. He also accuses the Vions of being hypocritical by causing pain by lacking the very emotions they are trying to evince from Gem. They agree, heal McCoy, and depart with Gem.