While on an astronomical survey, the unstable proto-nebula that the away team is studying flares up, damaging their shuttle and endangering their lives. During an attempt to beam back to the starship Voyager, a transporter malfunction occurs, and everyone's patterns merge briefly. All members of the away team successfully return to the ship, but the mobile emitter used by The Doctor is damaged. In an effort to diagnose the malfunctioning mobile emitter, it is secured in Voyager's science lab overnight while the computer performs a detailed diagnostic subroutine on it. Unknown to the crew, Seven of Nine's Borg nanoprobes infected the emitter during the transport and have begun to assimilate it. Later that night, Borg assimilation tubules spring from the emitter and begin to assimilate the lab console.
The next morning, Ensign Mulcahey, a member of the crew, goes to the science lab to check the results of the diagnostic subroutine run on the emitter. When he enters the lab, he is attacked by Borg extraction tubules. They do not assimilate him, but they do take a tissue sample from his body. On the bridge, Ensign Harry Kim detects an unauthorized transfer of power from the warp conduits to the science lab. Efforts to reach Ensign Mulcahey or anyone in the lab fail. When a force field with a Borg signature is detected in the science lab, Lt Commander Tuvok, a security team, and Seven of Nine are immediately sent to investigate.
The Voyager crewmembers discover the unconscious Mulcahey and a Borg maturation chamber containing a fetal Borg drone. Seven of Nine observes that her Borg nanoprobes were designed to adapt and assimilate any technology it encounters, and deduces that it is fulfilling its imperative by creating a new drone. The new Borg continues to age at a rapid rate, growing from a fetus to approximately six Earth years in only an hour.
After adapting the astrometric sensors to penetrate the Borg force field surrounding the maturation chamber, Seven of Nine is able to analyze the growing drone. The drone is basically a human male, having used Mulcahey's DNA as a biological template. The Doctor is concerned about getting his mobile emitter back, and demands that engineer B'Elanna Torres retrieve it immediately. Unfortunately, there is little she can do because the emitter is thoroughly integrated into the drone's cerebral cortex; removing the emitter would kill the drone. Tuvok notes that the Borg's implants are constructed of polydutonic alloy; Seven of Nine realizes that the alloy was extrapolated from the Doctor's mobile emitter, a piece of 29th century technology. The new Borg is essentially a 29th century drone, 500 years more advanced than any other Borg in existence. His reactive body armor, multi-dimensional adaptability, internal transporter nodes, multi-spatial force field, and other advanced abilities would make the Borg collective virtually unstoppable if they were to assimilate him. Seven of Nine is able to dampen the Borg's proximity transceiver so the drone cannot contact the collective.
Captain Janeway considers, and rejects, the idea of 'pulling the plug' and killing the growing drone. She knows the new drone poses significant security risks to the ship, but is troubled by the ethical ramifications. She also believes that there is a lot of scientific value in studying this unique drone individual. Janeway orders Seven of Nine to educate the drone in the ways of humanity as Seven herself was once instructed. Seven reluctantly complies.
The drone finishes maturing, and emerges from its maturation chamber as an adult. It sees Seven of Nine and mechanically demands that she provide it with its designation and purpose. Seven of Nine tries to make the drone realize that it is an individual, but it does not understand and continues to ask for its designation and purpose. She initiates a direct neural interface with the drone to instruct him, which works well initially. However, the drone soon takes over the interface, probes her neural pathways, and tries to assimilate all of her knowledge at once. Seven of Nine struggles to break free, but is no longer in control and cannot disengage the link. Tuvok attempts to disable the drone with a phaser but the drones shields prevents it. She commands the drone to stop, ordering it to comply, but he ignores her until she says, "You are hurting me." The drone abruptly terminates the interface.
Seven of Nine is able to activate the drone's linguistic database, so it is now capable of learning through language. The drone is also provided with Borg data nodes, which are safer and can transfer massive amounts of information via assimilation tubule. The drone is fascinated with the endless onslaught of data, and demands more. With the guidance of Seven of Nine and a few other crew members, the drone learns rapidly and grows closer to the crew.
As ordered, the drone arrives at Sickbay for a medical checkup. Upon observing the Doctor's medical equipment, the drone realizes that his Borg technology is extremely advanced and unique, and demands to know how that could be. The Doctor reveals that the drone is the result of a transporter accident. The Borg wonders, "An accident... Am I unwelcome here?"
The drone then reports to Captain Janeway's ready room to meet the captain. "One" is his new name, and he is adapting very well to life on Voyager, even to the point of developing a rudimentary personality. Janeway seems impressed, and later, when in the cargo bay, Seven of Nine tells him that he has "exceeded expectations." Shortly before they start their regeneration cycle together, One surprises Seven by thanking her for her help.
Their regeneration is interrupted when Capt Janeway, accompanied by a security team, wakes up Seven of Nine and informs her that the drone has transmitted a Borg proximity signal, and that an enemy vessel is approaching. Alarmed, Seven of Nine interrogates One, who denies sending any signal. After scanning One closely, she determines that his cranial implants have adapted and created a secondary transceiver, which sent its own signal without One's knowledge. In the past, One had expressed curiosity about the Borg, but his requests for information were always deflected because that knowledge was too dangerous. With a Borg ship only 3 hours away, it was now time to satisfy that curiosity with a crash course on the Borg collective. Janeway and Seven of Nine quickly educate One about the Borg and their nature. One expresses that he would like to try out the Borg collective consciousness, and asks if Seven of Nine would like to return to the Borg. She states firmly, "Voyager is my collective."
When a long-range tactical Borg sphere arrives at their location, One and Seven of Nine are able to hear the collective speaking in their minds. At Seven's insistence, One resists the temptation of perfection and attempts to enhance Voyager's shields and weapons. The enhancements are completed, but Voyager's technology is limited and it is not enough to save them from the Borg. One realizes that he must interface with the collective directly and disrupt them from within. He transports himself to the sphere, easily resists all attempts at assimilation, and then takes over their navigational controls. He steers the Borg vessel into the nearby nebula, which crushes the hull and destroys the vessel.
The Voyager crew, while happy to have defeated the Borg, are stunned by One's selfless sacrifice. Suddenly, Ensign Kim detects a life sign in the aftermath of the explosion; One's advanced multi-spatial force field protected him from the brunt of the explosion. His biological components, however, were critically injured. The severe trauma requires immediate surgery, but One refuses to allow it; his personal force field repels the Doctor's hypospray and any attempts at treatment. One explains that when he was linked to the hive mind, he learned that the entire collective was aware of his existence. He knows the Borg will pursue him relentlessly as long as he lives, endangering Seven of Nine and Voyager. One tries to reassure Seven of Nine by telling her, "I was a mistake... I was never meant to be." A visibly distressed Seven orders, "Lower the force field. You must comply." One refuses, "I will not." Seven of Nine begs, "You must comply. Please. You are hurting me." One looks at Seven compassionately, and replies, "You will adapt." One dies on the operating table, leaving Seven greatly saddened by his passing.