The senior officers meet and conclude that the symbiogenetic properties of the orchids the pair carried during transport caused the "merger" that created Tuvix. After the meeting, Tuvix attempts to adjust to his new identity, and Kes tries to adjust to Tuvix. Although she's drawn to him, she is unsettled by the amalgam's affection for her.

After Paris and Torres gather more samples of the alien orchid, they manage to confirm the method of Tuvix's creation by beaming together new plant hybrids, but are unsuccessful in their attempts to reverse the process. The Doctor admits he's not optimistic about bringing Tuvok and Neelix back as separate individuals. On hearing this, Kes mourns the loss of two men: her lover and her mentor.

Kes tells Janeway that despite Tuvix's wonderful qualities, she's not ready to let go of Neelix. Several weeks pass, and Tuvix settles into life aboard the ship. In time, Kes reaches out to him and apologizes for being distant. Just as it looks as if everyone has adjusted to Voyager's new crewmember, the Doctor announces that he's devised a way to restore him to his two original components. There's just one problem: Tuvix doesn't want to die, even if it means allowing the other two men to live.

Tuvix argues that he has a right to survive, and that restoring Tuvok and Neelix's lives amounts to his execution. The Doctor refuses to take Tuvix's life against his will, so in the end, Janeway is forced to take responsibility for performing the procedure. Tuvok and Neelix are fully restored, but Janeway's relief is tempered by the weight of her decision to end Tuvix's life.