When the Enterprise investigates a distress call from the planet Mulour (population 4 billion), Spock reports that sensors detect no life forms. There is no word even from Dr. Manway, head of a Federation science team on the planet, who has his own transmitter. The Enterprise's shields then come up automatically when it encounters a 1 meter long, 500 kg, cylinder which attacks the Enterprise with energy bolts having the strength of 90 photon torpedoes. Kirk torpedoes the object, but the energy is simply absorbed by the target. Kirk then transmits a message to the object, and it stops firing, requests communication, and allows itself to be beamed aboard the Enterprise.
The probe identifies itself as Nomad, and refers to Kirk as the creator. Checking records, Spock finds that a Nomad probe was indeed launched to explore the far reaches of the galaxy and seek out new life (and presumably to go where no probe has gone before). Apparently, Nomad believes that Kirk is Jackson Roy Kirk, the original creator of Nomad. Nomad insists, however, that his mission is to destroy that which is not perfect (including all biological ``infestations.'')
Kirk leaves Lt. Singh in charge of Nomad. When it hears Uhura singing over the intercom, however, it slips away to seek her out. Upon finding her, still singing, Nomad questions her as to what form of communication she was practicing. When she replies music, it erases her mind, calling her a mass of conflicting impulses. When Scotty tries to intervene, Nomad kills him. When Kirk is displeased, Nomad offers to ``repair'' the unit Scott, claiming that it was only acting in self defense. Kirk then asks Nomad to repair Uhura, which it claims it cannot since it has erased her memory banks. Nurse Chapel therefore begins re-educating her on how to read, and reports that she can be back on the job in a week, which doesn't speak too favorably for the training required for a Federation communications officer.
Kirk then tells Nomad to accompany two security guards to a waiting area (actually a top security cell). Spock attempts to study Nomad, but it only lowers its shields when Kirk explicitly tells it to. However, Spock is not able to learn full details from his scan, and therefore resorts to a Vulcan mind meld. How the analog-to-digital conversion is performed is not explained. Spock discovers that Nomad collided with an alien probe called Tan-Ru, designed to obtain and sterilize soil samples from other planets, and was severely damaged. Some of its memory was lost, and it subsumed Tan-Ru's directive, interpreting it to mean sterilize imperfections. Spock is shaken by the experience, and Kirk is forced to pull him away and tell Nomad to stop communicating. Kirk again confines Nomad to the cell, but it waltzes right through the security field and kills the two security guards when they attempt to stop it with phaser fire.
Nomad then makes his way to the engine room where it improves the ``efficiency'' of the engines 57% by increasing the matter-antimatter reaction rate. Kirk orders Nomad to reverse changes to the matter-antimatter reactor, as the Enterprise cannot stand the stress. Kirk confronts Nomad, telling him that his contempt of biological units is illogical, since its creator is a biological unit. Kirk tries to get the probe to return to the holding cell, but it kills the two security guards sent to accompany it and heads to sickbay. Here it examines Kirk's medical history, attacking Nurse Chapel when she tries to stop him. It then shuts down life support systems throughout the ship in order to destroy the imperfect units aboard it without destroying the Enterprise.
Kirk then gets Nomad to admit that it must sterilize everything which is in error. Kirk defeats Nomad by showing it its own imperfections: it thought he was Jackson Roy Kirk, it did not discover its mistake, and it did not exercise its prime function by eliminating itself because it was imperfect. While attempting analyzing the situation, Nomad is beamed into space. It is caught in a logic loop while attempting to analyze its errors, and finally self-destructs in order to ``sterilize'' its own imperfections.