During an Away Team survey of a planetoid that seems to be rich in raw dilithium, Neelix is attacked and left for dead. The other members of the team find him and beam him up to Sickbay, where the Doctor reports that the Talaxian's lungs have been removed. With no other alternatives, the Doctor fits Neelix with a set of holographic lungs. They'll keep him alive, but require him to remain confined in an isotropic restraint in Sickbay for the rest of his life.
Janeway leads an Away Team back to the planetoid, where they discover a medical lab filled with harvested organs. Unfortunately, Neelix's lungs are not among them. Minutes later, an alien ship speeds away from the planet, with Voyager hot in pursuit.
In Sickbay, a despondent Neelix is having difficulty adjusting to his situation, but he urges Kes to still go on with her life regardless. Voyager's Emergency Medical Hologram, still serving as the starship's only doctor, admits to Kes that he's having difficulty adjusting to the demands of being a full-time physician. Kes' intelligent, soothing advice makes the Doctor think that the Ocampan might make a good medical assistant.
When confronted, the aliens admit that they stole Neelix's lungs, but defend their actions by recounting the battle that their species — the Vidiians — have fought for years against the "Phage," a gruesome disease that destroys their genetic codes and cellular structure. Unable to defeat the Phage, they have learned to survive by scavenging organs from healthier species to replace their own diseased tissues. Unfortunately, Neelix's lungs have already been transplanted into one of the Vidiian's bodies. Unwilling to sentence the Vidiian to death to regain Neelix's chance for life, Janeway reluctantly releases the scavengers.
Grateful to the Captain for sparing them, the Vidiians offer to help Neelix with their superior medical technology. With their assistance, Kes is able to donate one of her lungs to Neelix, allowing him to live a normal life. After the successful procedure, the Doctor tells Kes that Janeway has granted permission for the Ocampan to begin training as a medical assistant.