Unimatrix Zero was a construct created by Borg drones that became mutated after their assimilation. While the mutation only affected 1 in over million drones, the mutated drones were connected to Unimatrix Zero via their interlink frequency and would enter the construct while undergoing their regeneration cycles and would be individuals again. When the cycle was completed, the mutated drones would enter reality, but have no memories of Unimatrix Zero.
Because the interlink frequency was based on a tri-axilating modulation, the Borg Queen was not able to detect it and destroy it. However, this all changed in 2376, when the Queen did become aware of Unimatrix Zero and set about finding the correct frequency so she could destroy it. She set about this by destroying mutated drones and studying their cortical array to find the correct frequency.
Aware that their destruction could be imminent, the inhabitants of Unimatrix Zero contact the ex-drone, Seven of Nine, aboard the USS Voyager. They asked Seven and Captain Kathryn Janeway if they could plant a nanovirus in the central plexus that would allow the mutated drones to keep their individuality in the real world. However, this became imperative when the Queen discovered the correct frequency and began sending drones to frighten the inhabitants.
Janeway agreed to help the inhabitants and she volunteered, along with Lieutenant Commander Tuvok and Lieutenant B'Elanna Torres, to be assimilated and plant the virus into the central plexus of a Borg tactical cube. While their plan was successful, it was decided that Unimatrix Zero had to be destroyed because the Queen was destroying all vessels when she lost contact with only a few drones. Together, Voyager and a liberated Borg sphere were able to disrupt the interlink frequency and destroy Unimatrix Zero with modified deflector pulses. (VOY episodes: "Unimatrix Zero, Parts I & II")