After losing contact with the planet Deneva (population 1 million) for more than a year, the Enterprise goes to investigate. Uhura's attempts to make contact at all frequencies, including private GSK783 subspace frequency 3, but without success. Spock consults the computer and discovers that waves of mass insanity have swept along a straight path through planetary systems Beta Portalin, Lavinius 5 (200 years ago), Theta Cygni 12, and Ingrahem B (2 years ago). Deneva (colonized a century ago and one of the most beautiful planets in the area) is the next planet on this path, and Kirk expects the worst for his brother Sam and his family.
While approaching the planet, the Enterprise encounters a Denevan ship heading straight for the sun. Attempts to convince the pilot to change course fail, and the pilot flies into the sun. Just before being vaporized, the pilot makes the cryptic statement ``I did it. It's finally gone,'' and claims that he is finally ``free.'' Uhura finally gets through to the private transmitter, and hears the message ``Please hurry, help us, I don't have much time. They'll know,'' being transmitted by Sam's wife Aurelan.
When Kirk beams down with a landing party, a group of armed men attempts to attack them with clubs, while at the same time shouting that they don't want to hurt them. Responding to a scream, the landing party finds Sam (who was a research biologist) dead and his wife Aurelan and son Peter in great pain. Aurelan refers to invaders, but the tricorder shows nothing unusual. After Aurelan and Peter have been beamed to the Enterprise and questioned as far as they can be, Aurelan reports that the invaders came from planet Ingraham B eight months ago after forcing the crew to take them there. She reports that the invaders use pain to control people and are forcing the residents of Deneva to build ships for them.
Kirk, Spock, and a landing party enter a building in which they find hundreds of small creatures which look like plastic pancakes. The creatures do not register on the tricorder and are highly resistant to phaser fire. When leaving, one of the creature whirls towards them and attaches itself to Spock's back. Back on the Enterprise, McCoy finds that Spock's nerves are being surrounded with strange tissue. Despite his incredible pain (as shown by the K3 indicator), Spock escapes from the sickbay and attempts to take over the bridge before being subdued and tranquillized. However, he is subsequently able to bring himself under control. He escapes again, and overpowers a transporter technician before Scotty covers him with a phaser. When he points out to Kirk that he is the reasonable choice to beam down to the planet to collect an alien for study since his nervous system is already compromised, Kirk allows him to go. On the planet surface, he is attacked by a man wielding a pipe, but is able to overpower him. He then phasers one of the alien pancakes and places it in a little red specimen box using a pair of plastic tweezers.
An analysis of the alien by McCoy shows it to be a one-cell creature resembling a brain cell. It seems also to be part of a larger organism which is composed of physically separate parts. McCoy tries to find the agent responsible for killing the creature when the Denevan ship flew into the sun. However, the alien seems unaffected by all radiation and heat, but McCoy initially neglects to try visible light. He finds that intense light kills the study specimen, and Spock volunteers to see if light also kills the alien material wrapped around his nerves. The experiment is a success, but Spock is blinded by the intense light. Seconds later, McCoy receives test results which demonstrate that the ultraviolet portion of the spectrum was all that would have been needed. The Enterprise consequently rings the planet with 210 ultraviolet trimagnesite intridium satellites (at 72 miles altitude), which bathe Deneva in ultraviolet radiation and kill the aliens. Meanwhile, Spock's eyes recover and his sight is restored because of a (hitherto unknown to us) Vulcan inner eyelid.