While attempting to find a faster way through the Nekrit Expanse, CommanderChakotay and Ensign Kaplan pick up a distress call with a Federation signature. When they land their shuttlecraft on the planet, they both come under fire from hostile natives who kill Kaplan and injure Chakotay. After he loses consciousness, a second group of colonists chases away the attackers and take him to the safety of their compound. There he wakes up with a woman by the name of Riley Frazier, who claims that the planet's inhabitants were some years earlier kidnapped by an unknown species and left on the planet. Suspicious of her insistence that he should stay in the room for the time being, he finds a way out and discovers that Riley and the other planet's colonists were not simply kidnapped but in fact assimilated by the Borg. When an electro-kinetic storm damaged their cube, their link with the hive mind was broken so they took what equipment they could and settled on the planet. Over time, they have regained their individuality and even removed most of their Borg implants, but a great deal of violent tension has arisen between the many different species which the Borg had assimilated.
Chakotay's injury worsens, and the only available cure is for him to be temporarily fitted with a neural link so that the former drones can exploit the medicinal properties of their retained collective consciousness. Despite his reluctance, he eventually agrees because it is clear he will otherwise die before Voyager arrives to rescue him. While connected to the miniature hive mind, he sees the other members' memories of their pre-Borg homes and families, and also learns of their hope that Voyager will be willing to reactivate a part of the Borg ship which will re-establish the harmonious neural link which had once united the planet's inhabitants when they were drones, so ending their social problems. When Voyager finally arrives (having found the buoy signal which Chakotay left above the planet before landing), Captain Janeway agrees to provide the former drones with food, medical supplies and upgraded security, but will not reactivate the ship for fear that this might draw attention from the Borg collective.
However, Riley and the others soon use their established link with Chakotay to make him reactivate the neural link anyway. As Janeway feared, this has unforeseen consequences as it reactivates the entire cube and some remaining Borg inhabitants whose link to the collective has not been severed. The rescue team sent to intercept Chakotay, along with Chakotay himself, are beamed aboard Voyager. The planet's inhabitants manage to order the Borg ship's self-destruct sequence to engage before it gains weapon capabilities. Within three seconds the ship explodes; but the mission was successful and the planet's inhabitants have regained their collective state. They send a message to Voyager thanking Chakotay for cooperating with their plans and release him from their link with their newly created "cooperative" which only affects the local inhabitants of the planet and no one else.
Chakotay discusses the situation with Janeway, and questions how long the inhabitants can retain a sense of morality amidst the power of a collective. After all, he reasons, it did not take them long to use him against his own will for their own motives. Janeway, struggling herself with the moral equation, cannot answer his question.
The possibility of a Borg drone's disconnection from the collective leading to the restoration of its individuality had previously been explored in Star Trek: The Next Generation (in particular, the arc begun in "I, Borg"), and would later become a major theme of Voyager with the introduction of Seven of Nine in Season 4.
Riley states that she was assimilated into the Borg collective after the Federation's disastrous defeat at the Battle of Wolf 359.
Jamahl Epsicokhan of Jammers Reviews calls Unity "a standout [Voyager] episode. The special effects are as good as I've seen them on Voyager, McNeill's direction is effective, the story is fresh and implicitly complex, the production is impressive, and the action and suspense works. This is not the best episode of Voyager, but it's among them."