A Borg fleet flees the destruction of a planet
The Borg-Species 8472 War was a brief by costly conflict from late 2373 to early 2374, fought between the Borg Collective and Species 8472. The forces of Species 8472 proved highly superior to that of the Borg, and their invasion of the Milky Way Galaxy was repulsed only after Captain Janeway of the USS Voyager provided the Borg with an effective weapon against them.
In mid-2373, the Borg Collective learned of the existence of a species whose physiology they believed represented the "apex of biological evolution." Designated Species 8472, this newly discovered race was the sole inhabitant of a realm known as fluidic space. Eager to assimilate this new species, the Borg entered fluidic space to add Species 8472's biological distinctiveness to their own.
However, the Borg soon found out that Species 8472's unique biology prevented them from being assimilated. Their immune system was so efficient, it destroyed the Borg nanoprobes before they could assimilate living cells. With their assimilation technology useless, the Borg were unable to adapt and unable to learn about their adversaries. Moreover, Species 8472's organically-based technology was extremely powerful. Their bioships were easily able to overwhelm Borg Cubes, and their armor was impervious to conventional weaponry. Species 8472 quickly removed the Borg from fluidic space.
However, Species 8472 did not stop there. They followed the Borg into our realm and pursued them to Borg controlled space. The Borg losses quickly mounted and found themselves completely outmatched. The Borg suffered losses to not only ships, but to entire planets.
At that time, the USS Voyager was reaching the area. The Doctor soon discovered a way to reprogram Borg nanoprobes to invade Species 8472's immune system. These nanoprobes would attack Species 8472 at the cellular level. Captain Kathryn Janeway made a deal with the Borg: Voyager would be escorted safely through Borg space and Voyager would provide the Borg with the necessary technology.
With the assistance of Seven of Nine, the Borg's representative aboard USS Voyager, a way to introduce the nanoprobes via photon torpedoes was found. With the misgiving of Commander Chakotay, USS Voyager was retrofitted with special launcher to fire the new weapons. The new weapon proved effective in battle, destroying all four attacking bio-ships. With this effective weapon in use, Species 8472 retreated back to fluidic space.