Part I

Seven of Nine dreams of a beautiful forest, which in reality is subconscious realm inhabited by the minds of certain Borg drones during their regeneration periods. Only a few drones possess the recessive gene required to experience the realm called Unimatrix Zero.

In the utopian Unimatrix Zero, Borg of various species and ages (including children) exist as their individual, unassimilated selves while regenerating on their Borg ships; when not regenerating, they revert to normal drones with no memory of time spent there. The Borg Queen is aware of Unimatrix Zero, considering it a disease, and destroys drones discovered capable of visiting there. However, the process of detecting affected drones is time consuming and she is eager to find a faster method of finding and deactivating them. Those who are detected are deactivated, dismembered, and studied in an effort to speed up the search.

Seven of Nine journeys with Captain Janeway, thanks to a double mind-meld performed by Tuvok, to Unimatrix Zero and reverts to Annika Hansen, her human identity before assimilation. She discovers she used to visit Unimatrix Zero when she belonged to the Borg Collective. Her forgotten lover Axum made contact with her so she may help them; the inhabitants of Unimatrix Zero have developed a masking nanovirus to inoculate them from detection by the Queen, but it can only be administered from the corporeal world. Seven is overwhelmed by her new-found emotions and denies them but eventually finds acceptance. If Unimatrix Zero cannot be stopped in the real world, the Queen plans to destroy it from within by sending drones to kill the subconscious, unassimilated drones.

As Voyager plans to help the Unimatrix drones, the Borg Queen makes contact to offer Janeway transwarp technology if Janeway ceases to help the Unimatrix drones. Janeway refuses and plans to infiltrate a Borg ship on her own and release a version of the nanovirus, now modified to allow the Unimatrix Zero drones to retain their memories and stage a resistance. After being blackmailed by Chakotay (he threatens to have the Doctor remove her from command if she insists on going alone), she, Tuvok and B'Elanna penetrate the Borg cube to reach the central plexus and administer the nanovirus but are caught. Voyager leaves them to be assimilated.

Part II

The Janeway, Tuvok, and Torres drones proceed with their plan to help Unimatrix Zero. They are not connected to the Borg Collective as the Doctor had inoculated them with a neural inhibitor, protecting their individuality. Tuvok's inhibitor wears off and the Collective eventually overcomes his mind.

The Borg Queen confronts Janeway to demand the drones of Unimatrix Zero submit themselves for reassimilation. The Queen destroys several of her own ships because only a handful of crew are "offline" and suspected of being the newly sentient drones from the dream realm. Janeway calls her bluff, pointing out that such a tactic would essentially require her to destroy the entire Collective. Having discovered a means of sending Borg as drones into Unimatrix Zero, the Queen threatens to release a Borg-modified form of the nanovirus from within Unimatrix Zero to kill every affected inhabitant's corporeal drone, unless Janeway agrees to speak with them.

Janeway informs her crew that Unimatrix Zero can no longer exist. Chakotay realizes this means destroying the matrix so the Queen cannot spread the nanovirus. Seven is forced to say goodbye to her lover, who is on a Borg ship in the Beta Quadrant. Voyager, aided by a Borg sphere crewed by liberated drones, rescues the away team. Independent Borg who now, like the Queen, have the advantage of being self-aware, take command of some vessels, rebel, and start a civil war with the Collective.