Unimatrix Zero is a secluded place within the Borg collective where drones can be themselves while they regenerate, but only certain Borg have the ability to visit. The Borg Queen considers Unimatrix Zero a threat because she does not want her Borg to ever have traces of individuality, but Captain Janeway thinks it could give the Federation allies within the Collective. Janeway, Tuvok and B'Elanna Torres put Borg implants in their bodies and infiltrate the Borg Cube to try and free the select few that are able to go to Unimatrix Zero, giving them the ability to maintain their individuality outside of Unimatrix Zero. The away team has been injected with a neural suppressant to keep their Borg implants from really connecting them to the Collective.

While the away team is on the Borg Cube, Seven of Nine goes to Unimatrix Zero herself to tell the Borg within what the team is doing. Seven had been able to go there when she was part of the Collective and she still maintains that ability. In the past, she had a romantic relationship there with her fellow Borg, Axum, and when she meets him there again, she notices those feelings returning.

While the away team is headed for the Central Plexus of the Borg Cube, Tuvok notices that his neural suppressant is wearing off and the Borg Queen begins communicating with him telepathically. The Queen finally convinces Tuvok to stop Janeway and Torres as they download a virus to free the select group of drones. They manage to get the virus into the system, but Tuvok prevents them from leaving. More Borg drones appear and capture Captain Janeway, but Torres is able to get away. Tuvok restrains Janeway and puts her in contact with the queen.

The Borg Queen makes Janeway watch on a viewscreen as she blows up a different Borg Cube, destroying the thousands of lives on board, because she lost contact with three of the drones due to Janeway's virus. The Queen uses the virus Janeway used to free the drones and alters it to actually kill the drones. She tells Janeway that unless the captain tells the free drones to rejoin the collective, she will go to Unimatrix Zero and kill all of the drones inside. Janeway is put into contact with Chakotay on Voyager to tell him the free drones have to go back to the collective, but instead of telling him that directly, she secretly tells him to destroy Unimatrix Zero. Without Unimatrix Zero, the Queen will not be able to find all of the free drones, and if she destroys all of the Borg vessels they are on, she will destroy her entire fleet.

After Seven tells everybody in Unimatrix Zero of the plan, they all agree that it is the best way to handle the situation and they offer to help get the away team back to the U.S.S. Voyager. While Voyager is preparing to attack the Borg Cube, a smaller Borg Sphere appears through a transwarp conduit and hails them. Korok, a Klingon that has been assimilated into the Collective, has taken over the Sphere and offers to help them destroy the Cube. Chakotay accepts his offer and both ships begin attacking the Cube. Just as the Borg Cube explodes, Harry Kim manages to beam Janeway, Tuvok and Torres back to Voyager where they can be relieved of their Borg implants.

Seven, meanwhile, has gone back to Unimatrix Zero one last time to say goodbye to Axum. Axum and Seven are the only people left as Unimatrix Zero falls apart around them. Axum tells Seven that he is on a Borg Cube in a totally different part of the galaxy and though it seem like they will never see each other again, he will find her. They both leave Unimatrix Zero as it completely fritzes out of existence.