"Scorpion" is a two-part episode of Star Trek: Voyager, the cliffhanger between the third and fourth seasons. It introduced Seven of Nine and Species 8472 to the series, and is generally regarded as the two most popular episodes of the entire series and its best cliff-hanger by Voyager fans. The first and second part both have an average rating of 4.5/5 on the official Star Trek website (as of March 3, 2008).
Quick Overview: Voyager makes a "pact with the devil" with the Borg in order to combat a new enemy.
This anecdote, many centuries old, is based on a fable mis-attributed to Aesop, The Scorpion and the Frog, in which the role of the fox is taken by a frog; in other respects the plot and moral are identical.
On the edge of Borg territory, which consists of thousands of systems, the crew discovers a narrow passage devoid of Borg activity. Dubbed the "Northwest Passage," it is filled with gravimetric distortions, but as Tom Paris puts it, "Better to ride the rapids than face the Hive." While the Northwest Passage appears safe, Janeway tells the crew that a confrontation with the Borg may be inevitable and instructs them to prepare for one. While Kes and The Doctor work on an antibody to combat the Borg assimilation nanoprobes, the Ocampan has a vision of dozens of Borg corpses.
Kes' premonition is followed by several more concerning the death of Borg and Voyager's destruction. Before Janeway can react, however, Harry Kim announces that fifteen Borg cubes are headed their way. The crew prepare for a fight, but the cubes ominously pass them by, as if they were not heading toward Voyager, but fleeing from something. As Janeway and Chakotay discuss the possibility that Voyager will be forced to remain in the Delta Quadrant, Tuvok informs them that the Borg ships' power signatures have stopped and the armada is dead in space. They follow the cubes' path only to discover that most of the cubes have been destroyed.
There is an alien bioship attached to the hull of one of the remaining cubes. Chakotay, Tuvok, and Kim beam aboard the cube to investigate, where they see the same image Kes described: dozens of Borg corpses piled on top of one another. They see no aliens but can hear roars coming from elsewhere within the cube. As they scan the bioship, Kes has a vision of Harry screaming in pain. B'Elanna Torres beams the away team back with the never before tried "skeletal lock" (locking onto the minerals in the away teams' bones) but not before the alien returns and injures Harry just as Kes predicted. The bioship detaches itself from the Borg cube and fires at Voyager but does not pursue it. Kes can hear the telepathic alien say, "The weak will perish."
Despite the new threat, Janeway decides Voyager must maintain its original course as the Northwest Passage is only a day away. The Doctor discovers along the way that an infection caused by cells from the alien is consuming Harry's body. He is unable to combat the infection with traditional medicine but thinks he can modify Borg nanoprobes to destroy the alien cells; however, it may be too late for Harry. Meanwhile, Tuvok and B'Elanna discover that the Borg call the alien Species 8472 and have been defeated by it several times. Upon reaching the Northwest Passage, Voyager is greeted by over a hundred bioships.
As before, Kes is able to hear the aliens say, "The weak will perish." They are arriving through some kind of quantum singularity, although it is unclear where they come from, they intend to destroy everything. Janeway considers the possibilities and comes up with a radical idea: an alliance with the Borg. Her plan is to offer The Doctor's cure to the Borg but withhold it until the Borg escort Voyager through their space. The crew does not question Janeway's judgment, but once the rest are gone, Chakotay admits he thinks what the captain is proposing is too great a risk.
Voyager travels to the nearest Borg star system, where a cube announces that it will assimilate the ship and places a tractor beam on it. Janeway explains the situation and the cube beams her aboard it. She and the Collective's voice are close to coming to an agreement when a quantum singularity emerges and ten bioships emerge. Ignoring several Borg cubes, the bioships head straight for a nearby planet. They emit a massive energy burst that obliterates the entire planet, and the cube, with Voyager in tow, narrowly escapes the resulting explosion.
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. When Seven implies that the drones on board could simply take the weapon and the ship by force, Chakotay 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.
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 pulled into space. Paris attempts to reverse course, but Voyager is pulled through the rift and into fluidic space.
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. The Doctor makes a joke about being two for two now having saved two of the bridge crew in under a week. Janeway asks to be left alone with Chakotay. After the Doctor is deactivated, she begins to demand 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 moves towards the console and throws Paris out of the way. She begins to assimilate the bridge controls, saying that Voyager would be assimilated. 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.