The Voyager remains on red alert after Captain Janeway, in exchange for safe passage through space, reaches an agreement with the Borg Collective to help them fight Species 8472, a race more malevolent than even the Borg. Although Chakotay strongly objects to the unpredictable collaboration, Janeway and Tuvok transport, with great caution, to the Borg cube. When a drone attempts to temporarily assimilate Janeway by connecting a neural transceiver to her, the alarmed Captain convinces them to instead choose a representative to communicate verbally with her. Soon a human Borg, designated "Seven of Nine", emerges to speak for the Collective. Janeway and Seven debate the use of weaponry, Janeway suggests photon torpedoes, but the Borg demand the use of a single large weapon. Suddenly a bioship appears and begins firing on Voyager. The Borg cube is hit as well, injuring Janeway. To prevent the destruction of Voyager, the Borg cube sacrifices itself and rams the bioship.
At the last moment Seven, Janeway, Tuvok, and several drones were transported to Voyager to continue their work. Janeway has been severely injured and the Doctor prepares to sedate her to protect her higher brain functions. Seven demands they continue to prepare the weapon. Janeway makes Chakotay promise to make the alliance with the Borg work, and to get the crew home. Chakotay however is convinced that the Borg won't honor their agreement. Seven, informed by the collective of the death of over four million drones in a massive loss in the middle of Borg space, now demands that Voyager reverse course and head for the central part of Borg Space.
Chakotay refuses, and gives new terms to Seven, namely that the Borg will be dropped off on an M-class planet on Voyager's journey with the weapon, and that a Borg ship could pick them up. Seven refuses, saying the Borg will lose the war by that time; however, Chakotay is not willing to listen to her and threatens to decompress the entire cargo bay at the first sign of resistance. Unsure of himself, Chakotay returns to the captain, who is still comatose. He finds it difficult to compel himself to work with such a total nemesis. Chakotay learns that the Borg sought out Species 8472 rather than the other way round.
Meanwhile, Seven begins opening the panels in the cargo bay Jefferies tube, accessing the navigational deflector. Kim alerts Chakotay, who demands Seven desist. Ignoring him, Seven opens a rift that begins pulling Voyager in. Chakotay, true to his word, decompresses the cargo bay. All drones except for Seven are blown into space. Paris attempts to reverse course, but Voyager is pulled through the rift.
Torres identifies the surrounding space as not space at all, but an organic fluid. Sensors read no planets, stars or any other phenomena. Seven orders Chakotay to meet her in the cargo bay. She informs him that Voyager must now face Species 8472 alone. They have been alerted to Voyager's presence and now are only nine hours away. Chakotay, still angered by her actions, receives another message to report to sickbay.
Janeway, up and about for the first time in days, is angry beyond words when Chakotay enters. After the Doctor is deactivated, she begins to demand to know why Chakotay did what he did. He tries to relate to her that he felt the Borg were changing the agreement, but she disagrees with his actions. The two reach an impasse, one that threatens everyone. However Janeway has an idea...
Later, Seven is escorted to the bridge. Janeway is back in command, and informs Seven that Chakotay is confined to the brig. This is a situation that Seven prefers. She agrees to work with Seven to upgrade Voyager's systems with Borg technology, and then sets the crew to create the weapons needed and upgrade the ship within the allotted time. When the bioships arrive, Voyager is ready for them. The first warhead used seems to have little effect, but after a short delay all the attacking ships are destroyed.
Seven shoves Harry Kim out of the way and takes Voyager back to normal space once more, but upon reentering, they find a swarm of bioships converging on them. This time Janeway orders a high-yield warhead and all of the bioships are damaged or destroyed. The rest of the ships flee, and Seven is informed that the Borg have prevailed. Suddenly, Seven attacks Paris and begins to assimilate the bridge controls. Janeway orders Chakotay to start operation 'Scorpion'. Chakotay, by use of a temporary neural link, confuses Seven just long enough for Torres to short out the console, disabling Seven and knocking her unconscious.
Hours later, the crew has resumed course, and all seems well, but the Captain is still troubled. Seven, still with her Borg implants, is seen unconscious in sickbay, her Borg components still active.