Scorpion (Star Trek: Voyager)

Voyager is approaching Borg territory. The territory covers thousands of star systems and is too big to go around, but they find a narrow path through the sector that the Borg avoid likely due to the numerous gravimetric distortions within it. The senior staff agree that it is better to ride through this path, dubbed the "Northwest Passage", than to face the Borg directly. Captain Janeway orders preparations for a Borg encounter. While helping the Doctor craft antibodies to disable Borg assimilation, Kes has a brief vision of a pile of Borg corpses. She starts to experience several more, all based around the destruction of the Borg and Voyager.

As they near the Northwest Passage, 15 Borg cubes travel towards them at high speeds, but ignore and pass them. Shortly afterwards, scans indicate that the cubes have been swiftly destroyed. Janeway orders the ship back to investigate. They find a bioship is attached to a portion of a Borg hull. An away team transports over to discover a pile of Borg corpses, just as Kes had seen, and alien roars elsewhere on the ship. As they try to scan for the source, Kes has another vision, this time of Ensign Harry Kim being attacked. Janeway orders an emergency beam-out just as an insect-like creature strikes at Kim. The bioship detaches from the hull and fires at Voyager as they flee the area, the near-miss negatively affecting the ship. Kes reports hearing a voice say, "The weak will perish".

Janeway orders the crew to continue course for the Northwest Passage. Analysis of the Borg's logs shows that the alien species is catalogued as Species 8472 and has defeated the Borg many times before. The Doctor is able to eliminate the alien infection in Kim's body using modified Borg nanoprobes. Eventually Voyager reaches the Northwest Passage, only to find a fleet of bioships waiting, with more emerging from a quantum singularity. After moving to a safe distance, the senior staff discuss their options. Janeway proposes a temporary alliance with the Borg to face a common threat, offering the Doctor's cure for the Species 8472's infection as a bargaining chip. The staff is dubious but agree it is their only option.

Voyager travels to a nearby Borg-occupied world, and is met by a Borg cube. Janeway announces their intentions, and the Borg beam her to their ship, where she begins negotiations. Suddenly, a fleet of bioships appears nearby and destroys the Borg planet. The Borg Cube, with Voyager in tow, narrowly escapes its destruction.

The Borg accept Janeway's offer of the modified nanoprobes in exchange for safe passage through their space, and she and Tuvok begin discussions. However, the Borg find verbal communication to be inefficient and attempt to attach a neural probe to Janeway. Janeway stops them by suggesting they choose a representative Borg for her to speak through, citing that they did this once before when they turned Captain Picard into Locutus. A drone calling herself Seven of Nine emerges as the chosen representative. As they discuss the integration of the nanoprobes into weaponry, a bioship appears and opens fire on the ships, injuring Janeway. The Borg transport Janeway, Tuvok, Seven, and several drones to one of Voyager's cargo bays before ramming the bioship with the cube, destroying both of them. Janeway's injuries are so severe that she needs to be sedated and undergo urgent neurosurgery; before she is, she makes Chakotay promise to maintain the alliance.

Seven learns from the Collective that Species 8472 have killed millions of Borg and several planets in the middle of their territory, and demands Chakotay direct Voyager to help. Chakotay refuses, since this would significantly deviate from their course, and states his intentions to strand the Borg on an M-class planet to be picked up later. Seven is able to access the ship's deflector dish from the cargo bay and uses it to create a subspace rift. Chakotay orders the cargo bay depressurized, jettisoning all the drones into space except Seven who manages to stay. Though the crew regain control of the dish, the rift has grown large enough to draw Voyager into it.

Voyager finds itself in "fluidic space", a liquid filled place where Species 8472 originate. Seven asserts to Chakotay that since he refused to help, Voyager must face Species 8472 alone, revealing that the Borg started the war when they tried to assimilate them. Their argument is stopped when Janeway announces she has recovered and retakes command of Voyager. She has Chakotay placed in the brig for disobeying orders (but really to appease Seven) and continues work on the weapon, as several bioships are detected heading towards them. The modifications are completed in time, and they are able to destroy the attacking ships.

Seven reverses the process that drew Voyager into fluidic space, but the ship appears in the middle of a bioship fleet. They quickly reapply their modifications to a large-scale weapon that destroys most of the enemy fleet and forces the rest to flee. Seven then turns on the Voyager crew and tries to assimilate the consoles. The crew have prepared for this — Chakotay uses a neural relay to distract Seven long enough for Torres to electrify the console, knocking Seven out and breaking her connection to the Collective. Voyager resumes its course for the Alpha Quadrant with an unconscious Seven onboard.