Leutenant Tuvok and Neelix of the U.S.S. Voyager are returning from a botanical scout mission when a bizarre transporter malfunction fuses them into a single being on a molecular level. The merged being has the DNA of both men, and traces of a third, plant-based genetic pattern from an alien orchid the two were gathering on the planet below. The man who emerges from the transporter is tall, with dark speckled skin, the ears of a Vulcan and a combined Starfleet-Talaxian uniform. He says that he is Tuvok - and that he is Neelix - but what he becomes forces the Voyager crew to grapple with questions of personal rights, individuality, and life and death.

Tuvix realizes that he has all the memories and character traits of his Vulcan and Talaxian "parents," but combined into a third, separate consciousness. Tuvix reasons that his "birth" was due to symbiogenesis - a process where organisms reproduce not by pollination or mating, but by merging with separate species on a microcellular level to produce a third organism.

Tuvix quickly becomes a valued member of the crew, solving security problems faster than Tuvok, forging relationships with the other officers and becoming a more skilled cook than Neelix. Eventually the Doctor and Ensign Harry Kim discover a way to restore Tuvok and Neelix by using the surgical transporters to separate Tuvix's DNA patternse Tuvix, however, doesn't want to die, and refuses to undergo the separation. He believes he has a right to live, and argues that the procedure would be murder, an execution for a crime he didn't commit.

Captain Janeway finally decides to save her two crewmen. Tuvix pleads with his crewmates on the Bridge to help him, but in the end is subdued and led to Sickbay. The Doctor refuses to perform the separation against Tuvix's will, so Janeway performs the procedure with the surgical transporters herself. With a long last look at his crewmates, Tuvix dissolves, and Tuvok and Neelix emerge from the transporter beam fully restored.