The USS Enterprise is pursuing a course of tremendous madness that has had a significant impact on multiple planets, leading to the downfall of their societies. Finally, they draw near Deneva, a Federation colony where Captain Kirk's brother, Sam, is stationed alongside Sam's wife, Aurelan, and their son, Peter. After entering the system, they try to halt a vessel as it swoops into the local star, its captain screaming about being "liberated" before the ship is obliterated.

The Enterprise crew, headed by Kirk and First Officer Spock, along with Chief Medical Officer Dr. McCoy and a security team, travel to the main city of Deneva. Upon arrival, they are met by a group of men wielding clubs who warn them to leave. When the men attack, Kirk has them stunned. However, Dr. McCoy finds their brains are still experiencing violent stimulation. The team discovers the home of the Kirk family and finds that Sam (played by William Shatner) is dead, Aurelan (Joan Swift) is acting erratically before passing out, and Peter (Craig Hundley) is in a coma. Kirk and McCoy bring the survivors back to the Enterprise, where it is discovered that they are suffering from a similar condition to their attackers. McCoy provides them painkillers, and Aurelan briefly wakes up to tell Kirk about "things" spreading from planet to planet, using other bodies to fabricate ships.

Kirk goes back to the world and works together with Spock to search for these organisms. They find a group of single-celled animals affixed to the walls and roof of a structure. The creatures can fly and attempt to attack the people; the arriving gathering finds they are almost impervious to phaser fire. One of them communicates with Spock before Kirk can pull it off, and Spock falls in agony. They transport back to the Enterprise, and McCoy finds that the creature has infused some of its tissue into Spock's spine; it will be difficult to extract it surgically. When Spock regains awareness, he attempts to take authority of the vessel, yet McCoy sedates him in time. Later, Spock apologizes to Kirk and expresses that his mental control can manage the torment, yet he should return to the surface to acquire a specimen to examine. Upon his return to the settlement, Kirk and McCoy agree that Spock can stun a creature. Reaching the Enterprise, Spock and Kirk decide that the creatures are a part of collective intelligence.

Spock and McCoy are unsuccessful when trying to get rid of the creature. Kirk convenes a senior staff gathering and stresses that they must find an answer before the creatures arrive at the next populated planet with over one million dwellers, a response that will not harm the hosts. He recollects the vessel's pilot declaring that he was liberated before plunging into the sun and suspects the sun's features may hurt the creatures. He realizes that they have yet to test out visible light as a way to conquer the animals.

At first, a trial of dazzling light caused the patient's death in the medical center. Spock then offered to be subjected to a powerful illumination without eye protection to demonstrate that a being that infected its host could be annihilated. Although the experiment was successful, Spock became blind. After studying the initial test, it was concluded that only ultraviolet light was needed to exterminate the creature. The Enterprise then irradiated the settlement with ultraviolet light from a set of satellites, eradicating the organisms on the planet and clearing the survivors of the parasites. As the Enterprise got ready to leave the orbit, Spock declared that his Vulcan inner eyelids had prevented permanent blindness, and he could see again.