After Janeway is abducted and Voyager is being tractored on a Borg vessel, escaping from debris from a planet destroyed by the Borg's enemy, Species 8472 in Scorpion, Part I, Janeway has announced the new alliance with the Borg. The alliance insures Voyager helping them to build a weapon involving Borg nanoprobes, in return, the Borg have granted Voyager passage through their space.

Meanwhile, the Doctor finds out that Species 8472 are accessing Kes's memory, and making her have visions of her being attacked by them. Janeway decides to change course to throw them off a bit.

Later on, an attacking 8472 vessel destroys the Borg Vessel, but not before Janeway, Tuvok, their Borg representative Seven of Nine, and some other Borg drones transport to the Cargo Bay. Janeway, when on the cube, was hit with an electrical beam and falls into a coma. When the acting captain Chakotay denies taking the Borg back into their space, they react by setting off a burst from the deflector which takes them into Species 8472's domain. Janeway quickly recovers and tells Chakotay that his decisions were wrong. After the 8472 ships damage Voyager, Voyager sets off the nanoprobic weapons they have been working on, and destroy the ships. But, when Voyager exits their domain, they are intercepted by hundreds of 8472 ships. Janeway decides to fire the wide-beam torpedo that destroys many of their vessels, and the others retreat. After that, Seven of Nine tries to assimilate the ship, but Chakotay stops her by telepathically linking their thoughts. When her connection to the collective is severred, Voyager leaves with Borg technology all over their ship, and a new crewmember... Seven of Nine.