Scorpion (Star Trek: Voyager)

Voyager's crew discover from long-range probes that they are approaching a sector of space occupied by the Borg. The Borg occupation covers thousands of star systems, but they find a narrow path through the sector that the Borg avoid due to the numerous gravimetric distortions within it. The senior staff agree that it is better to ride out through this path, dubbed the "Northwest Passage", rather 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 Borg and Voyager.

As they near the Northwest Passage, they find 15 Borg cubes rapidly approaching. The crew prepares to engage but the ships travel past them at high speeds. Shortly after they pass, the Borg ships no longer register on their scanners, and Janeway orders an investigation. They find the ships have been destroyed, while 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 of Ensign Harry Kim being attacked. Janeway orders an emergency beam-out just as an insect-like creature strikes at Kim. Aboard Voyager Kim is raced to Sickbay. The bioship detaches from the hull and fires at Voyager as they depart 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. Lt. Tuvok and Chief Engineer B'Elanna Torres analyze the Borg's logs to find that the alien species is cataloged as Species 8472 and has defeated the Borg many times before. The Doctor is able to eliminate the infection in Kim's body using a potent modification of Borg nanoprobe. Eventually Voyager reaches the Northwest Passage, only to find a fleet of bioships waiting with more appearing through the gravitational distortions. After moving to a safe distance, the senior staff discuss their options. Janeway comes up with the radical idea of an 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 lays waste to the Borg planet. The Borg Cube, with Voyager in tow, narrowly escapes its destruction.

The attack by Species 8472 leads the Borg to accept Janeway's offer in exchange for safe passage through their space towards the Alpha Quadrant, and she and Tuvok begin discussions. However, the Borg, believing verbal communication to be inefficient, attempt to attach a neural probe to Janeway through assimilation. Janeway stops them, and instead suggests they choose a representative Borg for her to speak through. Soon, a drone calling herself Seven of Nine emerges as the chosen representative. Janeway and Seven resume discussions on how to deal with Species 8472. As they discuss the development of specialized weapons, a bioship appears and starts firing at the ships, and Janeway is injured. The Borg transport Janeway, Tuvok, Seven, and several drones to one of Voyager's cargo bays before ramming the bioship, destroying both of them. The Doctor finds Janeway's injuries very severe and needs to fully sedate her to protect her higher brain functions. Janeway makes Chakotay promise to maintain the alliance with the Borg before she is sedated.

Seven and the drones are working on assembling the weapon when she learns from the Borg Collective that Species 8472 have killed over 4 million Borg in the middle of their sector, and demands Chakotay direct Voyager to help. Chakotay refuses, since this would significantly deviate from their course home, 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, causing all of the drones but Seven to be lost to space, while she is forced to abandon her access to remain aboard. 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", where Species 8472 originate from according to Seven. Seven asserts to Chakotay since he refused to help, Voyager must face Species 8472 on their own, revealing that the Borg started the war with them. Their argument is stopped when Janeway announces she has recovered and taken command of Voyager again. After having Chakotay placed in the brig, Janeway starts working again with Seven to prepare a weapon to defeat the bioships and perform other upgrades on the ship, as several bioships are detected heading towards them. The modifications are done in time, and they are able to destroy the attacking ships.

Seven reverses the process that drew Voyager into fluidic space, but the ship returns to normal space 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 the surviving ships flee. After learning that the Borg have prevailed in their fight, Seven then turns on the Voyager crew and tries to assimilate the consoles. Janeway, having prepared for this, tells Chakotay to start "Operation Scorpion". Chakotay uses a neural relay to distract Seven long enough for Torres to electrify the console, knocking Seven out. Voyager resumes its course for the Alpha Quadrant, but Janeway is still unsure about their alliance with the Borg and Seven's true allegiance.