Seven of Nine awakens from a "nap" in an uneasy state. She dreamed of a beautiful forest with trees and flowers. In this place people knew her as Annika and she was almost human. Seven is not used to "dreaming" so she is unsettled by the experience.
Paris, thinking he is being reprimanded by the crew for being late, is surprised by being awarded an Officer's Pip. He is then reinstated to Lieutenant by Captain Janeway.
Seven retires again to her alcove wearing the cortical monitor the Doctor gave her and closes her eyes. She finds herself back in the beautiful forest. She tells herself that this is "not real" when suddenly a voice is heard assuring her that it is. It is the voice of Axum, someone she has seen before in this environment. He calls this place Unimatrix Zero.
Axum explains to Seven that Unimatrix Zero is a place where the Borg Drones go during regeneration so they can exist as individuals. The Collective knows about this place but cannot find it. The Drones who visit Unimatrix Zero have the recessive mutation that the Borg Queen is trying to find and destroy.
Axum informs Seven that she used to visit Unimatrix Zero before she escaped the Collective. She too has the recessive mutation that only one in a million Drones has. Axum tells her that the Collective has found a way to detect them, so it is only a matter of time before they find enough of the Drones to isolate the interlink frequency and demolish Unimatrix Zero.
Axum begs Seven for her help, even though she is no longer a part of the Collective. Seven is their only hope because unlike her, after the Drones complete their regeneration they have no memory of Unimatrix Zero.
When Seven awakens she informs the crew of what she encountered. The Doctor confirms that she was not just having a dream, she never reached REM, therefore what she is telling the crew is real. Seven asks the Voyager crew for their help to save Unimatrix Zero.
Meanwhile, the Borg Queen is coming closer and closer to finding Unimatrix Zero. She has continued to dismantle other Drones in order to observe their parts and find a way into Unimatrix Zero.
Janeway feels that the crew should help, because it is a new aspect of the Collective and a potential weakness. They begin coming up with a plan to help the Drones.
Tuvok suggest a Vulcan technique known as the "Bridging of Minds," Janeway agrees. Janeway, Seven, and Tuvok will be hooked up to monitors. Tuvok will oversee their thoughts and Janeway will go with Seven back to Unimatrix Zero.
Upon their arrival they find Drones, sent by the Borg Queen, trying to destroy Unimatrix Zero. A battle ensues and Janeway defeats the last of the Drones. The Borg Queen has seen the fight through the eyes of a regenerating Drone and does not like what she sees. Janeway assures Axum that they will help defeat the infiltration of the Borg Queen's Drones into Unimatrix Zero.
Janeway and Seven begin working on a plan to help Axum and the others. The crew is trying to find a way to deploy a highly experimental "nanovirus" designed to target all the Drones with the recessive mutation and reprogram their memory centers. That way, when they leave their alcoves they will retain their memories. Janeway tells Seven to go back and reassure Axum that they are working on a plan and will be there as soon as they can.
Seven arrives at Unimatrix Zero and things have gotten worse, however the Klingons have banded together and are fighting off the Borg Queen's Drones. Axum confesses to Seven that they were involved before she escaped the Borg. They had promised not to leave one another, but as things got worse Axum insisted that she leave him behind and save herself. Although Seven feels familiar with Axum and Unimatrix Zero, she still does not remember what he is talking about.
Back on Voyager, Janeway is preparing to transform herself into a Drone in order to implement the nanovirus, Chakotay does not think it is a good idea. While they are arguing, the power beings to flicker and the command center becomes dark and foggy. The Borg Queen appears on the screen and threatens Janeway and her crew by informing them that she knows they have been in contact with Starfleet. The Queen informs Janeway that if she becomes involved with helping Unimatrix Zero, Voyager will have a difficult time making it home. Janeway does not back down, frustrated, the Borg Queen disappears and the crew knows they are going to have a fight on their hands.