Realizing they have entered Borg space, the crew attempts to plot a course through a corridor that seems devoid of Borg activity, which they dub "the Northwest Passage." As the Doctor and Kes research methods of fighting off Borg assimilation, Kes is troubled by recurring visions of dead Borg and the destruction of Voyager.

Suddenly, the ship is surrounded by an armada of the cube-like Borg vessels. But then the armada mysteriously retreats, leaving Janeway to wonder, what would make the Borg run? Not long after, Tuvok and Kim discover that the power signatures of the Borg cubes, which they've been tracking, have terminated. Tuvok finds an unknown weapons signature in the Borg debris, which raises another question: what could do this to the invincible Borg?

Sensors pick up odd bio-readings from the outer hull of one of the cubes, and Janeway sends an away team to investigate. On the defunct vessel, the team finds a pile of Borg bodies that look the way Kes saw them in a premonition. When Kim senses an alien presence on the ship, Kes "sees" him screaming in agony. Janeway orders them back and the team is transported just as a fierce lifeform attacks Kim. As Voyager races away, Kes informs Janeway that the alien, communicating telepathically, told her "the weak will perish."

In Sickbay, Kim's body is infested with alien cells that entered his body in the attack. The Doctor reprograms Borg nanoprobes in the hope of negating the damage. Meanwhile, Torres discovers the alien lifeform, known to the Borg as "Species 8472," has taken over the Northwest Passage, and Kes senses an invasion is planned. With their former plan no longer an option, Janeway faces a terrible choice: retreat into the Delta Quadrant and forget about getting home, or confront the Borg and risk assimilation.

After considerable thought, Janeway comes up with a third alternative. She will offer the Borg a way to defeat Species 8472 in exchange for safe passage through Borg space. Janeway is beamed aboard one of the cubes, where she presents her proposal. Suddenly, Species 8472's bio-ships begin firing at the Borg cubes, and at Voyager, which is locked in the grip of a Borg tractor beam . . .