Starting off with the giant tribble in the room, the biggest issue fans have with what Janeway did, was not that she sided with the Borg and helped them survive, but that she did so by committing genocide. Species 8472, the designation given to this alien race by the Borg, were some of the nastiest aliens found within the Star Trek universe, a bunch of extra-dimensional apex predators. They were, despite first appearances, incredibly intelligent, and came from a dimension known as fluidic space, which was accessed by the Borg in an attempt to assimilate them through quantum singularities. They were, despite being organic, immune to assimilation, and the Borg’s attempt was considered an act of war. They drove the Borg out of their space, and followed them into the Federation/Borg dimension, with the explicit aim of Borg xenocide.
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This might seem, at first, like a good thin. The Borg have been primarily villains throughout their tenure on Star Trek, a terrifying force hell-bent on assimilating and destroying cultures. They seemed to be unstoppable, with the Federation only able to hold them back rather than defeat them properly, they were always a looming threat in the background. Species 8472 offered a solution, if the crew of the USS Voyager had simply sat back and allowing them to wipe the Borg out. Species 8472’s aggression wasn’t even unjustified or unprovoked — the Borg had invaded their space and tried to assimilate them. Bt of course, things for Captain Janeway were never simple.
The biggest issue with allowing this plan to unfold was that Species 8472 were really nasty. Janeway did consider the idea of letting them destroy the Borg, consequently making the universe a much better and safer place, but this all ended when she met a member of the species. They were ruthless and attacked without provocation. All attempts to communicate were met with the words “the weak shall perish” — a motto on par with the Borg’s “resistance is futile.” Before she left the show, the character Kes managed to make telephonic communication with them, which resulted not only with her being seriously injured, but led her to reveal their nefarious plans: Species 8472 would not stop at ending the Borg, but would continue to “purge” the galaxy. Considering how effectively they were killing Borg, something the Federation had been struggling to do for years, they were a considerable threat to all life in the universe.
Their plan to wipe out all life in the galaxy stemmed from their desire to never allow another living organism to enter their fluidic space, as the Borg had opened a door that could be opened again. Species 8472 just wanted to be left alone, and they would annihilate anyone that could potentially jeopardize this. It thus makes sense why Janeway did what she did. Faced with two highly powerful foes that stood in her way to return home, she made a deal with the more reasonable one. What’s more, they had worked out an effective way to wipe out Species 8472. They had found a way to harness what were basically bioweapons, moderating nanoprobes created by the holographic doctor, but could not use them on the scale needed to stop 8472. Thus, they partnered up with the Borg, who used the weapon in exchange for relatively free passage through their space.
Many fans take issue with the way in which Janeway sided with the Borg, the use of a genocidal biological weapon used on nightly intelligent sentient beings truly being the icing on the cake. However, there is a resounding consensus that overall it was the right decision to make. The Borg were powerful and terrifying, and continued to pose a real threat to the Federation, but it’s a case of “better the devil you know.” The Borg, in all their culture absorbing, assimilating glory, were a far better option than the ruthless desolation and xenocide at the hands of 8472, who had made it clear that they would not stop until every living organism that was not a member of their race was wiped out.
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