The crew is sitting in the mess hall for a celebration in honor of Tuvok, who is promoted to lieutenant commander. After the party Tom Paris catches up with B'Elanna Torres. The two haven't talked since the incident with the warp core three days ago, and Tom decides to make a move. B'Elanna confirms that she meant what she said when she confessed her love for him, and Tom accepts this with a kiss.
Shortly after the party ends Voyager receives a distress call. It's a hologram alone aboard a ship. His six flesh-and-blood crewmates have been killed and he requests assistance. The Doctor is eager to meet a fellow hologram and he and B'Elanna take off in a shuttle to meet the disabled ship. When they beam on board, all is quiet. The hologram stalks them for a few moments while they try to establish what is wrong with the ship. When he comes face-to-face with them he is nervous, suspicious, and distraught. He introduces himself as an "isomorph". He says his crew suddenly died of a virus and he doesn't know what to do next. B'Elanna gets to work trying to stabilize his matrix so he can stay visible.
Meanwhile back on Voyager Harry Kim has been assigned to work with Seven of Nine. She correctly notes that he seems "apprehensive" at the prospect. Despite his wariness of her frightening Borg behavior, he seems to be developing a bit of a crush on her, and he is distressed by the idea of working closely with her. They manage to get their work done, but they are interrupted when Seven cuts her hand on a piece of equipment. Tom Paris, who has recently been recruited as the Doctor's new assistant, mends the cut in sickbay. He notices that Harry is growing fond of her, and advises him to keep his distance.
B'Elanna has some trouble with the isomorph, who is emotionally labile and unpredictable. One minute he giggles at her need to sustain herself by consuming food ("you nibble like a fish!"), and the next he unleashes an angry tirade about the disgust he feels toward "organics". B'Elanna excuses herself and catches up with the Doctor, insisting that they leave the ship and the disturbing hologram behind. The Doctor brushes her off, suggesting she be more patient with the isomorph, who is simply lonely and lacking in appropriate communication skills. B'Elanna doesn't buy it, and heads off to locate the hologram's main control center.
As she explores other decks of the ship the isomorph accosts the Doctor and pours out his heart. He has felt like a slave to the organics, who are weak and unsanitary and require ridiculous amounts of maintenance and hygiene just to keep functional. He has grown to hate them and is glad he has the ship to himself. He begs the Doctor to come with him and teach him how to use the ship and be free of organics forever. The Doctor starts to realize why B'Elanna is uncomfortable around this angst-ridden isomorph.
B'Elanna finds the matrix controls. She also finds the bodies of the crew, who were not killed by a virus. They were violently murdered. Before she can shut down the homicidal hologram he appears behind her and grabs her. He thrusts his hand into her body and grips her heart.
Back on Voyager Harry is trying to get closer to Seven. He asks her out to the holodeck. She has textbook knowledge of human behavior and immediately understands that he is attempting to spark romantic interaction between them. Since romance is irrelevant, the goal-oriented Seven suggests they proceed directly to copulation, and directs him to remove his clothes. Thoroughly unnerved, the embarrassed Harry retreats.
B'Elanna's Klingon physiological backups are keeping her alive despite the isomorph's having perforated her cardiac muscle, but she'll need to get back to Voyager`s sickbay soon. She and the Doctor try to disable the crazed isomorph. He makes a grab for the Doctor's mobile emitter, but B'Elanna manages to jolt him with a high-voltage cable, which destabilizes his matrix for good. They hurry off the ship. Safely back in Voyager's sickbay, the Doctor patches up B'Elanna and she feels more than well enough to take Tom Paris back to her quarters.