In a vast alien metropolis on a planet called Quarra, Kathryn Janeway enters a power distribution plant and reports in to a shift supervisor, who takes her to a workstation and explains her task. Janeway has taken a job among a multi-species workforce with no recollection of her previous life as captain of Voyager. When she has trouble working the controls, another worker named Jaffen comes over to help and tries to befriend her. They are chastened for fraternizing by Seven of Nine, who knows herself as "Annika Hansen" (her human name), the new Efficiency Monitor. Jaffen doesn't return to his station until he invites Janeway to go out for a meal after work, but she turns him down.
Meanwhile, Tom Paris — also unaware of who he really is — gets himself hired in a local tavern to wait and bus tables. That night Jaffen is in the tavern telling an anecdote to some friends, and he gets an uproarious laugh from Tuvok, whose behavior is very atypical. Janeway comes in, supposedly to eat alone while she studies manuals, but Jaffen joins her, and he ends up walking her home. They live in the same building, and he invites her to his place; she turns him down.
The next day, Janeway learns that all the workers must periodically receive inoculations to protect them against radiation. As a squeamish Tuvok is getting injected, he has a flashback of himself in his Starfleet uniform, struggling against a Quarren doctor giving him an injection. The strange memory leaves him trembling and perspiring.
All this time Chakotay, Harry Kim and Neelix have been in the Delta Flyer on a trading mission with the Nar Shaddan. When they return, Voyager is not at the rendezvous point. The starship is disabled inside a nebula, and the Doctor is the only crew member on board and is trying to make repairs. When the others find the ship and come aboard, the Doctor explains what happened: Voyager hit a subspace mine which deluged the ship with poisonous tetrion radiation, so Captain Janeway ordered the crew into escape pods, leaving the Doctor in charge of the ship as the Emergency Command Hologram. The Doctor then had to fend off scavengers trying to claim the abandoned vessel, and hid inside the nebula. He since discovered that the subspace mine was a deliberate attempt to disable Voyager. And he hasn't heard a word from the rest of the crew.
At the power plant, Tuvok has another flashback: He and Janeway were brought into a Quarren medical facility where a Dr. Kadan claimed to be treating Janeway for "Dysphoria Syndrome"; when Tuvok demanded her release, Kadan had him restrained and "inoculated." Shaken by this flashback, Tuvok approaches Janeway and says they know each other, that perhaps they met in the hospital, but she has no recollection of a hospital or of knowing him prior to her job. He gives up as Jaffen steps in, who makes dinner plans with Janeway. Meanwhile, Torres is sitting alone in the tavern, and Paris tries to get to know her. He asks to get together with her, but she reveals that she's pregnant, although unmarried, and leaves. The four people aboard Voyager complete repairs and begin searching for their crew. Kim finds them on a class-M planet less than three days away, and they set course. Janeway and Jaffen have their date, where dinner is a disaster. But it doesn't matter — they fall in love and kiss.
Voyager arrives at Quarra and Chakotay speaks with an ambassador who will not allow him to communicate with his crewmates. The ambassador says they are leading safe, comfortable lives there, and any attempt to disturb them would be met with force. Neelix learns there is a severe labor shortage in the Quarren system, so Chakotay gets the idea of applying for jobs themselves so they can infiltrate the plant where their people are working. Because he has spoken with authorities and could be recognized, Chakotay has the Doctor alter his features to look non-human, and he and Neelix prepare to go to the planet undercover, with subdermal transponders that will allow them to transport through the shield grid.
At the power plant, "Annika Hansen" orders Tuvok to go get the inoculations that he's been neglecting. Tuvok speaks her Borg name — "Seven of Nine" — and tries to mind-meld with her to make her remember herself. But security guards grab him and take the desperate Vulcan away. Chakotay secures a job at the plant and immediately approaches Janeway. She doesn't recognize him, so Chakotay continues the ruse of being a happy new employee. Neelix runs into Paris at the tavern, keeping up the same ruse, unable to jar his friend's memory. After Chakotay meets up with Neelix, they follow Torres in the streets and grab her. Kim beams Neelix and the struggling Torres up to Sickbay, where the Doctor tries to help her. Meanwhile Jaffen asks Janeway to move in with him, and she agrees. Tuvok is in the Quarren hospital where Dr. Kadan tells him he's experiencing "Dysphoria Syndrome" and will feel better after an injection. Chakotay is being pursued by security guards, but Kim can't beam him up because the ship has fallen under attack. The guards chase Chakotay through the facility up to a precipice overlooking the massive city, and he finds himself trapped.