Unimatrix Zero is a part of the Collective that certain drones have access to while regenerating. Only those drones with a particular recessive gene have this access. In Unimatrix Zero, these drones can act as individuals. However, while the drones are active they retain no memory of their individuality, or of Unimatrix Zero. (See The Drones of Unimatrix Zero)
The Borg Queen held Unimatrix Zero to be a threat as it allowed drones to retain a part of their individuality. When Voyager became aware of Unimatrix Zero, through Seven of Nine, Janeway saw it as a way of acquiring allies within the Collective.
Janeway, Tuvok and Torres disguised themselves as drones and infiltrate a Borg Cube in an attempt to locate and liberate the drones with access to Unimatrix Zero. In doing so they hoped to be able to allow these drones to retain their individuality outside Unimatrix Zero.
Janeway’s team had been given a neutral suppressant to avoid becoming connected to the Hive Mind. However, Tuvok’s neural suppressant began to wear of and the Borg Queen was able to communicate with him. The Borg Queen was eventually able to convince Tuvok to stop Janeway and Torres from freeing the drones. Tuvok failed to stop them downloading the virus that would release the drones, but did not allow them to leave the Borg ship. Janeway was captured, and Tuvok put her in contact with the Borg Queen. Torres managed to avoid capture.
The Borg Queen forced Janeway to watch the destruction of a Borg vessel because there were three liberated drones onboard. This also lead to the destruction of thousands of her drones.
The Borg Queen altered the virus Janeway introduced to kill the targeted drones, rather than liberate them. The Queen threatened the Unimatrix Zero drones with an invasion of Unimatrix Zero if they did not return to the Collective.
The Queen forced Janeway to contact Voyager so that Seven of Nine would tell the drones of this, but Janeway secretly told Chakotay to destroy Unimatrix Zero. If it did not exist, the Queen would have no method of locating the liberated drones. Destroying every ship these drones were on would lead to the destruction of the Borg fleet.
The drones agreed that the destruction of Unimatrix Zero was the best plan and offered to assist in returning the away team to Voyager. Korok, an assimilated though now liberated Klingon, was able to take control of the Borg Sphere on which he was stationed. He brought it to where Voyager was preparing to attack the Borg Cube. The two ships then destroyed the Cube, but not before Kim was able to beam Janeway, Tuvok and Torres back to Voyager where they could have their Borg implants removed.
When Unimatrix Zero was finally destroyed, Seven of Nine and Axum were the only two drones left there. They had had a relationship there while Seven was still part of the Collective and were there to say their final farewell. Axum discovered that his Borg Cube was in another part of the galaxy from Voyager, but promised to find Seven again.
The outcome of the liberation of these drones is unknown, but it is believed that an underground movement was started.