A disguised Chakotay is being pursued by Quarren security officers and is trapped at a forcefield. He smashes a control panel to disable the forcefield, then overpowers the guards and escapes, but not before getting a phaser shot in the arm. Meanwhile, Harry Kim and the Doctor are in command of Voyager as it is being fired upon by Quarren patrol ships. They disable the first two ships, but five more approach and they are forced to retreat. The injured Chakotay enters the tavern where a brainwashed Janeway has just decided to move in with her new boyfriend, Jaffen.
A Quarren investigator named Yerid enters the tavern inquiring about two people who disappeared earlier that evening — named B'Elanna and Neelix. The waiter, Tom Paris, points him to Chakotay, but he's already disappeared. In the Quarren hospital, Dr. Kadan orders a skeptical Dr. Ravoc to do a memory sequencing treatment on Tuvok. Meanwhile in the power plant, Seven of Nine is on the job and has a flashback of life on a Borg cube. Connecting the flashback to her encounter with Tuvok earlier, she goes to her Supervisor's office and asks about him. Yerid arrives to inquire about the two missing employees, saying he believes that Amal Kotay — Chakotay's assumed identity — is responsible for their disappearance.
Janeway moves her things to Jaffen's apartment, but when she returns to her old place she finds Chakotay hiding out there. He tells her that B'Elanna and other people in the city were brought to the planet against their will and made to forget their real lives, and he's trying to help them. Janeway reluctantly lets him stay, and decides to do something about his injury. Voyager, meanwhile, has hidden in a moon's crater to make repairs and to treat Torres for her altered memory. Neelix takes Torres to her quarters to re-introduce her to her real life, and she is surprised to learn that the waiter from the tavern is her husband. At the plant, Seven catches Janeway taking a dermal regenerator, but she promises to return it. Seven is sidetracked when she has an opportunity to enter the Supervisor's office and use his console; she learns that Tuvok has accessed numerous employee files including Janeway's, B'Elanna's, and her own. Janeway returns to Chakotay to heal his injury, and he reveals that he's from a ship called Voyager. Chakotay observes that she seems happy in her job and her life, but she seems capable of so much more. Janeway responds that she wouldn't want more responsibility. Chakotay is contacted by Voyager through his subdermal transponder, and they inform him that the ship is two days away but need the planet's shield grid disabled so they can transport the crew members back. Chakotay tells Janeway that she's the captain of that ship, but she has a hard time believing him. To prove himself, he takes the dermal regenerator and undoes the alterations made to his face, revealing that he is the same race as she. He tells her they are also friends.
Janeway tells Jaffen the story she just heard, but he thinks Chakotay is trying to manipulate her with promises of a better life. Meanwhile Chakotay is found by Yerid and is taken in for questioning. Chakotay tells him they are both investigating disappearances, and has questions of his own. Just then Dr. Ravok enters with orders to transfer Chakotay to Neuropathology to be treated for mental illness. As he's taken away, Chakotay tells Yerid the truth about himself and his abducted crewmates.
On Voyager, Kim and the Doctor are discussing tactics and arguing over whether the Doctor should remain a Command hologram, when they are hailed by Chakotay. He says he's almost ready to shut down the shield grid, and gives instructions on where and when the ship should enter orbit. They don't know that Chakotay is being subjected to a mind control device and is sending them into a trap.
At the tavern, Seven meets discreetly with Yerid to share her findings that more than a hundred employees — most of the same species — began work on the same day, which is unusual during a labor shortage. Also, they were all processed through the Neuropathology division, including herself, which she doesn't remember. Seven wants Yerid to interview Tuvok in the hospital, but Yerid reveals he was relieved of duty that morning. So Seven goes to the hospital herself and visits with Dr. Ravoc, reporting that she's been having "disturbing thoughts." Ravoc looks up her file and sees she was previously treated for Dysphoria Syndrome. She asks to speak to an expert on the condition, so Ravoc steps out to get Dr. Kadan. She takes that opportunity to use his computer. Meanwhile, Yerid contacts Janeway and asks to know everything Chakotay told her.
At the hospital, Kadan is enraged that Ravoc allowed Seven to access restricted files and leave. Ravoc is suspicious that an apparent "outbreak" of Dysphoria Syndrome occurred under Kadan's watch, and realizes that he had made false diagnoses on patients, altered their memories and sent them to work at the power plant. Kadan admits it's true, but claims it was to cure the labor shortage and improve the patients' lives. Ravoc threatens to report him, but Kadan says the authorities are behind him. Meanwhile, Paris harbors Seven, Janeway, Jaffen and Yerid at the tavern, who are collaborating about Chakotay's story and how to prove it. Janeway and Jaffen go to the power plant to use a subspace transponder to contact Voyager, while Seven and Yerid return to the hospital to help Chakotay and Tuvok.
With Jaffen's help, Janeway succeeds in hailing Voyager, where she sees B'Elanna in uniform and hears Kim call her "captain." B'Elanna asks her to find a way to shut down main power so the shield grid will be disabled. Just then Voyager comes under attack by three ships, and Janeway is surrounded by security guards. Jaffen helps her evade them, then she works the computer to make it think the reactor core is overloading so it'll automatically shut down main power. Meanwhile in the hospital, Seven and Yerid point a weapon at Kadan to force him to release Chakotay and Tuvok from the mind control devices. On Voyager, Kim gets the idea to use three escape pods as armed decoys to disable the attacking ships. They succeed, and B'Elanna gets the transporters back on line. Janeway's own plan works, and power goes out all over the city. With the shield grid down, Voyager beams up all of its crew members. The Doctor treats them and they recover, but in the meantime he, Kim and Neelix confer with Yerid and the Quarren Ambassador about undoing the conspiracy, with a promise that all of Kadan's "patients" will be treated and repatriated. Janeway says a final good-bye to Jaffen, then resumes her role as captain and takes Voyager on its way.