The story involves Dr. Phlox, whom Captain Archer orders to grow a mimetic symbiote as the source of a transplant for Chief Engineer Tucker when an injury threatens Tucker's life. Meanwhile, Tucker lies unconscious in Sickbay.
The symbiote is born, and Phlox names him "Sim." By the end of the episode, however, the story becomes tense: Phlox must perform the transplant before the end of Sim's fifteen-day lifespan, and, according to Phlox, the procedure will be fatal to Sim. Phlox makes this startling discovery only after Sim's genesis; previously, Phlox had calculated that the procedure wouldn't interfere with Sim's lifespan. Sim vehemently protests the procedure; he expresses a strong desire to live through the rest of his natural life—Tucker's own life notwithstanding. In a conversation with Archer, Sim desperately tries to persuade him to forbear his death, but Archer would rather he voluntarily submit to the procedure. "You're not a murderer," Sim says in the scene, to which Archer replies, "Don't make me one."
The story is further complicated when an experimental procedure is revealed, involving a certain enzyme, that might allow for an extension (presumably by decades) of Sim's lifespan. Apparently, Phlox was aware of this procedure, but he concealed his knowledge of it; according to his sensibility, its uncertain nature precluded it from being worthwhile even to consider.
Sim eventually volunteers himself to the transplant once and for all, but before he does, several events, important to the plot, take place:
Sim visits Main Engineering, so that he may spend time with activities he loves most: maintaining the warp engine, and being in the presence of Sub-commander T'Pol, toward whom he has outspokenly developed romantic feelings.
Later, in a scene immediately prior to the transplant procedure in Sickbay, T'Pol gives Sim a kiss. The cause of her non-Vulcan action would be explained in later episodes.
Sim nearly escapes in a shuttlepod. When he makes the attempt, Archer is alerted on the command bridge to an unauthorized presence in the shuttlebay. Archer then visits the shuttlebay directly, and finds Sim leaning against one of the shuttlepods in a contemplative, though resolved, pose. Sim immediately confesses to considering escape, but then says he finds the idea of spending the rest of his life in a shuttlepod unattractive.
After Sim has undergone the procedure, and after Tucker has been rejuvenated, the final sequence occurs: Archer honors Sim's sacrifice in the presence of part of the crew (including Tucker), and Sim's body is ejected into space.