As Voyager plans to help the Unimatrix-drones, the Borg Queen contacts the ship. She knows of Voyager's recent communications with the Federation and offers Janeway transwarp technology, if Voyager is accommodating and ceases helping the Unimatrix-drones. Janeway refuses. After being blackmailed by Chakotay (he promises to have the Doctor remove her from command), Captain Janeway, Tuvok and B'Elanna penetrate the Borg cube to reach the central plexus and administer the nanovirus. Voyager distracts the Cube while they infiltrate the cube but are caught. Voyager leaves them to be assimilated. The cliffhanger episode of Season 6 ends there.
In the continuation in Season 7, it is revealed that they allowed themselves to be assimilated because the Doctor had inoculated them with a neural inhibitor, which protects their individuality. However, Tuvok's inhibitor wears off and the Collective eventually overcomes his mind.
The Borg Queen confronts Janeway, demanding that the drones of Unimatrix Zero submit themselves for reassimilation. The Queen destroys several of her own ships, each housing thousands of lives, because only a handful within are "offline" and therefore 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, she then threatens to release a Borg-modified form of the nanovirus from within Unimatrix Zero which would kill every affected inhabitant's corporeal drone, unless Janeway agrees to speak with them.
The captain thus informs her crew that Unimatrix Zero can no longer exist. Chakotay realizes that the statement is meant literally - destroying the matrix so the Queen can't reach the affected drones as easily, as well as cutting the Queen's only way to spread the nanovirus. The drones within are informed beforehand. Seven is forced to say goodbye to her lover, who is on a Borg ship far away in the Beta quadrant. Meanwhile, Voyager, aided by a Borg sphere crewed by liberated drones, manages to rescue the away team. The episode ends as the independent Borg, who now, like the Queen, have the advantage of being self-aware, take command of any vessels they can, rebel, and start a civil war with the Collective.