As Voyager readies for a potentially dangerous encounter with the Botha, the Doctor orders an exhausted Captain Janeway to take some "R&R" in the holodeck. Janeway tries to get into her favourite holonovel, a story in the fashion of Jane Eyre, but before long, she is called back to the Bridge for first contact with the Botha. The Bothan representative gives the crew a chilly reception, but sets up a rendezvous to determine whether or not they will allow Voyager to pass through their space. Aboard Voyager, Captain Janeway starts seeing characters and objects from her holonovel. Later, Janeway thinks she sees Beatrice, the little girl from her holonovel, in one of the ship's corridors. Unable to attribute Beatrice's appearance to experiments the crew is performing on Voyager's imaging systems, Janeway wonders if she's seeing things.
Janeway goes to see Neelix to review her routine and see if anything she saw was real. She reviews the lunch menu, and ends with cucumber-sandwiches with fine china tea-cups. Neelix points out that there wasn't any cucumber-sandwich as she recalled or fine china tea-cups. Janeway goes to sick-bay and the EMH Doctor can't find a single thing wrong with her brain. After Kes is asked to get a medical tool for the Doctor, Janeway sees Beatrice and then Kes sees Beatrice, too. The Doctor orders Janeway to her quarters for rest until he can determine the source of this event. Later, after Janeway hears the voice of her fiancè, Mark from Earth, she's attacked with a knife by Mrs. Templeton, another holonovel character, cutting her hand in the palm. Again, Kes confirms the event, only for it to be a hallucination while Janeway is still in sick-bay from the previous scene.
Janeway puts Chakotay in charge of meeting with the Botha while she undergoes medical testing. Once again, the alien representative is hostile and this time, his ship engages the crew in a battle, leaving Voyager damaged. Leaving Sickbay, Janeway races to the Bridge, where the Bothan is on the viewscreen. Soon afterwards, the crew begins entering a catatonic state one-by-one, with only Kes and the Doctor remaining unaffected. She's stunned to see it is Mark, at least, that is how it looks to her. However, on the same viewscreen, Tom Paris sees his disparaging father, Admiral Paris (not the same actor who plays Admiral Paris in later episodes); Harry Kim sees his girlfriend Libby; and Tuvok sees his wife T'Pel. Each having separate visions based on each of their perspective characters.
B'Elanna Torres contacts Janeway from Engineering and reports that the crew seems to have fallen under some kind of psychoactive trance, the result of a bio-electric field emanating from the Bothan ship. Chakotay arrives to aid Torres, but communications seem down. Nonetheless, even as she begins working on a way to block the field, she falls prey to its spell: her and Chakotay in a romantic embrace. On the Bridge, Paris finally succumbs to the trance and Janeway heads to deck 11, seeing Chakotay entranced in the turbo-lift. As Janeway's illusion of Mark kisses her, she becomes a victim, as well, and can no longer move freely.
Kes and the Doctor are all that remain of the crew. Kes, whose telepathic abilities allow her to resist the field, and the Doctor are left to block the mysterious force that is disabling the ship help the others to stop the psionic-field causing this. Kes realizes that she is slowly being affected by this illusion when Paris tries to keep her from Engineering. Kes calls the Doctor, informs him of the situation. Neelix arrives, but Kes sees he is a hallucination when he tries to stop her. She resists and manages to complete Torres' work which restores the crew to normal.
A telepathic Bothan confesses to having caused the disturbance, because he could; but, he disappears before they can learn anymore from him. As they continue on their way, the crew reflects uneasily about what is lurking in the subconscious corridors of their minds.