The Enterprise is exploring the Argolis Cluster, an area the Federation is considering for colonization. While there, they detect a signal of unknown origin and, naturally, investigate. Upon arriving at the signal’s origin, Riker leads an away team into what turns out to be the wreckage of a Borg ship and finds a single survivor.

The away team reports in and Riker and Picard agree that the best course of action is to simply get out of Dodge. Crusher, however, isn’t having it and begins treating the Borg’s injuries, hoping to give him a chance of surviving long enough to be rescued (this even as Picard makes clear in no uncertain terms that doing so would be a sure fire way to alert the Borg rescue party to their presence). His hand forced (and unwilling to follow Worf’s cold-blooded suggestion of simply killing him), Picard orders the survivor brought aboard. As Crusher examines the Borg in the Brig, Picard asks LaForge about the possibility of introducing an invasive program into the Borg’s programming before returning him to the hive. The Borg’s interconnected nature would cause this program to spread throughout the Collective, theoretically dealing a crippling blow to their neural network.

At a staff meeting, LaForge estimates that – if they are able to successfully construct and introduce an invasive program, the Borg could suffer “total systems failure” in a matter of months. Crusher says what no one else seems willing to, that they’re talking about destroying an entire race. Picard agreed that such a thing would normally be unconscionable, but argues that the Borg leave them little choice. They are interrupted by a report from the brig. The Borg is awake and Crusher and LaForge are tasked with seeing to his needs, and the doctor notes that he almost seems scared in his isolation. Meanwhile, during a fencing match, Guinan questions Picard about the wisdom of harboring their “guest”. The captain explains Crusher’s humanitarian concern and that he hopes it was the right call. In the next round, Guinan feigns an injury, disarming Picard and scoring a touch when he drops his guard to help. “You felt sorry for me,” she tells him. “Look what that got you.” In the brig, LaForge and Worf enter the Borg’s cell to install a power conduit (so that it can “eat”). For the first time, the Borg – who identifies himself as Third of Five -speaks. In a typically Borg fashion, he tells the officers as they work that they will be assimilated and insists that “we” must be returned to the Collective.

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To aid in developing the invasive program, LaForge has Third of Five brought to the cybernetics lab for perceptual tests, with which Crusher reluctantly assists. As they run the tests, they converse with him and find he possesses an almost childlike curiosity. In the course of the conversation, the two address Third of Five as “you,” which he assumes to be his name. Inspired, LaForge suggests “Hugh” and the name sticks. As the tests continue, Hugh expresses his puzzlement at humanity’s resistance to assimilation. He tells them that he is lonely here, that he misses the voices – the thoughts of the other drones – that he constantly hears on a Borg ship. Later, LaForge has second thoughts, which he voices to Guinan.

The normally sympathetic bartender is standoffish, berating LaForge’s sympathy for Hugh and stunned at the fact that he named the Borg. Before leaving, LaForge suggests that Guinan actually speak with – or just listen to – Hugh. On the bridge, sensors detect an incoming Borg scout ship.

Guinan arrives in the brig, having taken LaForge’s advice. She tells Hugh about what the Borg did to her people and is taken aback when he actually sympathizes. Later, in the lab, LaForge and Hugh talk some more, the latter still not quite understanding why humans don’t want to be assimilated. LaForge explains the value of individuality and self-determination, and when he explains friendship (as a counter to loneliness), Hugh points out that this describes their relationship.

Later, LaForge and Data present the finished program to Picard, though the engineer voices his newfound reservations. Picard isn’t convinced, evoking the lab rats of old. That evening, Guinan visits Picard’s quarters and urge him to talk with Hugh. Picard seems unmoved, but the next day he has Hugh brought to the ready room. Hugh recognizes the captain as Locutus and he decides to play the part, telling Hugh that he is here to facilitate the assimilation of humanity. But instead of the Borg responses that Picard clearly expected, the confrontation instead highlights Hugh’s individuality, culminating in his first use of the word “I.”

After this encounter, Picard calls a staff meeting. He has reconsidered the plan and is seeking other options. The plan now becomes one of banking of the possibility that Hugh’s newfound sense of self “infecting” the rest of the Borg upon his return – assuming he wants to return. And so, Picard and LaForge present Hugh with a choice. He can either stay aboard the Enterprise or return to the crash site to await the Borg rescue party. The choice overwhelms him. He wants to stay with LaForge but ultimately decides to return to the crash site in the hope of protecting his new friends from Borg retribution. LaForge accompanies Hugh to the surface, where they say their farewells. The Borg arrive and collect Hugh, who looks to LaForge as they beam out.