The USS Enterprise was sent to respond to a call for help from the Malurian star system. Despite recent communications, Spock reported no life readings from any of the 4 billion inhabitants when they arrived. Suddenly, the ship's shields were up when a small cylinder-shaped object fired off a powerful energy bolt equivalent to 90 photon torpedoes. Captain Kirk ordered to counterattack, but the object soaked up the energy. Finally, after a few more attacks, and with the ship about to be destroyed, Kirk made contact with the object. After some back-and-forth communication, the object requested a face-to-face conversation with the Captain and allowed itself to be transported to the ship.

The " Nomad " object recognized Captain Kirk as "the Creator." Spock informs that a Nomad probe was launched by Earth during the early 21st century with the mission to explore the universe and find new life forms, yet its destruction had supposedly been reported – something that Spock doubts. The present Nomad has mistakenly taken Kirk as Dr. Jackson Roykirk, the maker of the initial probe. Nomad's new task is to kill any "biological infestation" it considers imperfect, including the entire populace of the Malurian star system. Nomad states that it did not need to destroy the Enterprise since "the Creator" was on board.

As Nomad was under the responsibility of a crew member, it slipped away to examine the sound of Lieutenant Uhura singing, which it identified over the intercom. When it arrived on the bridge to ask questions, it requested Uhura to "concentrate on music" while searching her mind, eliminating her memory. When Chief Engineer Scott attempted to intervene, Nomad terminated him, claiming self-protection. After realizing Kirk couldn't fix Scott, Nomad offered to bring him back to life. Unfortunately, Nomad healed Scott but couldn't "restore" Uhura's memory loss; thus, Nomad was taken to the brig. Since Uhura's brain was not harmed (just her memories were cleared), the medical staff started to re-educate her (by the end of the episode, Uhura was almost back to normal).

Spock uses a Vulcan mind meld with the machine to gain additional insight. Afterward, he finds that Nomad had a run-in with a meteoroid, which caused severe destruction. Later, the probe encountered and assimilated with Tan Ru, an extraterrestrial tool devised to collect and clean soil specimens from various planets. Nomad adopted Tan Ru's mission protocol, taking it to mean "purge any imperfections." The amalgamation of the two probes gave Nomad the authority to annihilate life in an entire star system. Captain Kirk likens Nomad's transformation to the changeling myth, a tale in which a human baby is swapped with a fairy infant, with the latter taking on the persona of the previous.

When the Nomad probe escaped its holding cell, it injured two guards who had been trying to keep it confined. It proceeded to the engineering deck, where it augmented the engines to a level far beyond the regular maximum warp speed. As soon as the Captain showed up, Nomad reported that the engine efficiency had increased by 57%. The Captain immediately ordered it to undo the modifications since the other parts of the Enterprise couldn't bear the raised speed. The probe followed the command.

Frustrated with Nomad's bias towards imperfect "biological units," Kirk highlights that its own "Creator" is a biological unit. Nomad said it needed to be "reassessed." So Kirk instructed the probe to go back to the brig, and it left with a security guard. Spock then cautioned Kirk that admitting to Nomad that he, "the Creator," is not flawless may have been a misstep. Spock also noted that because Nomad had threatened to return to its "starting place," the Earth and all its inhabitants were now in danger of sterilization.

On its way to the brig, Nomad eliminated its two guard escorts and decided to go to sickbay instead. After reviewing Kirk's medical records and verifying his physiological shortcomings, Nomad was done with its "reassessment." It then moved on to engineering, incapacitated crew members, and disabled the ship's life-support systems, leaving the Enterprise with limited time to function.

Captain Kirk reappears and disputes the probe anew, querying it on its mission. When Nomad says its order to wipe out flaws allows no exceptions, Kirk points out that Nomad itself needs to be revised, mistaken in identifying Captain Kirk as its actual creator Jackson Roykirk. He then states that Nomad has made two other mistakes, not detecting its blunder and not purging itself as faulty. Nomad commences contemplating the consequences of Kirk's assertions, which drastically taxes its systems. Kirk and Spock rush to the transporter room with Nomad and, with a concluding command from Kirk to "carry out your main function," beam it into deep space. Seconds after transport, an explosion is detected near the Enterprise, and Nomad is gone. The episode concludes lightheartedly, with Kirk proclaiming that he is pleased that his "son" Nomad, having cured Mr. Scott, could have made a great doctor.