After recent events, USS Voyager still remains without working warp propulsion and is infested with Borg technology. Seven of Nine, the Borg drone saved from the destruction of her cube, has her connection with the Borg collective severed. She is now able to function as an individual, but she is shocked by the change and still refers to herself in the first person plural. Her body starts to heal and reject Borg technology. The Doctor decides that he should remove her Borg implants so she can recover.
The Doctor hesitates to operate on a patient who refuses medical attention, but Captain Janeway, who believes that Seven of Nine is unable to make decisions for herself in her current state, convinces him to do it. During the operation, she starts to have a seizure, caused by an implant in her brain. Kes uses her increasingly powerful telepathic abilities to disable the implant and stop the seizure.
The Doctor removes some of the technology, but Seven of Nine is upset by the result. She is not used to being an individual and she repeatedly demands that she be returned to the Collective. Janeway refuses, and asks her to help with removing the Borg technology in Voyager's systems.
Meanwhile, Kes and Tuvok meditate. Kes has learned to manipulate matter on a subatomic level, and begins to see beyond even that.
As Seven of Nine begins her work on repairs she is closely guarded by Harry Kim and a security guard. While looking at the hardware, Seven sees a transmitter, and her Borg impulses are sparked into action by the stimulus. She pushes Ensign Kim out of the room, shuts the door and barricades herself in the room. She accesses a subspace transmitter, and tries to send a message to the Borg. Kes senses that something is wrong, and uses her abilities to send an electrical surge that stops Seven.
Seven is held in the Brig, where she has a long talk with Janeway about her separation from the Collective. Meanwhile Neelix and Kes talk about their past. She tells him about her new powers and demonstrates them. Neelix is hurt as the table they were sitting behind starts to change. The ship's structural integrity begins to destabilize. When Janeway and Tuvok enter the room, they see Kes on the floor and her body changing - destabilizing at the subatomic level, as Tuvok explains. The Doctor is unable to explain this reaction, he only knows that her powers must be suppressed or she might die.
Seven of Nine tries to unsuccessfully break through the Brig shielding door. Janeway comes inside her cell with information about her past. Before assimilation, she was a human girl named Annika Hansen. The new information enrages her and her wish to return to the Borg remains unchanged.
Kes and Janeway have their last talk and Kes is overcome by a fit, her powers warping her very surroundings. She cannot control herself and becomes a danger to the ship. She and Janeway agree she should leave the ship before it is destroyed. Kes boards a shuttle and puts some distance between herself and Voyager.
As her atomic structure destabilizes, she contacts Voyager and tells them she is about to give them a gift. As she vanishes, Voyager's warp core begins to function at more than 120%. The ship hurtles through space, ending up over 9,500 light years away in a flash. The crew realizes they are ten years closer to home. With their friend Kes far away and on another plane of existence, the crew try to accept Seven into their midst. She reluctantly accepts their help.