Neelix directs the crew to a planet supposedly rich in dilithium, but during an away-team survey, he is attacked by a humanoid alien who surgically removes his lungs. Transported to Sickbay, Neelix's only hope is a pair of holographic lungs programmed by the Doctor. Even so, the lungs are temporary, at best: Neelix cannot move in the machine, which resembles an iron lung. Janeway, Kes and the others do the best they can for his spirits; Kes stays with him and decorates the ceiling so Neelix has something to look at.

In the meantime, Janeway heads a search for the aliens, the Vidiians, that leads to an asteroid that serves as a base. When confronted, the aliens admit to stealing Neelix's organs, but defend themselves by telling the story of the "phage," a bizarre disease that attacks their people, eating away at their bodies and organs until they are forced to scavenge others as substitutes. When prodded to return Neelix's lungs, they are told that they have already transformed them for their own use.

With no alternative, Janeway is forced to let them go. The aliens, taken by this gesture of good will, agree to help Neelix, and perform an emergency lung transplant with a willing donor, Kes. Because of Kes' interest in medicine, the Doctor asks Captain Janeway for permission to train her as a Medical Assistant.