During a test on the warp engine, Trip is seriously injured and falls into a coma. His heroic actions do save the ship from a breach, but Enterprise sustains damage and is left drifting in a dangerous polaric field. Phlox is concerned that Trip may not survive, and poses one potentially controversial alternative: using one of his creatures, a Lyssarrian Desert Larvae, Phlox could clone Trip with a simbiot, then use its neural tissue for a transplant. The simbiot would have Trip's genetic make-up, but it would grow old and die in a span of 15 days. Archer is uneasy about this plan, but he eventually decides that he has no choice: he must complete his mission and he needs Trip to do so.

Phlox acts as a surrogate father to the simbiot, dubbing him "Sim" and caring for him as the baby quickly matures to a boy, a teenager and an adult over just a few days. Despite having his own life, Sim retains all of Trip's memories. Eventually, Archer has to inform him of his true purpose. Sim seems to take it all in stride, though the strangeness of his situation begins to have an effect on him as he matures into adulthood. As he grows up, Sim finds himself becoming part of the Enterprise crew.

As Phlox and Sim wait for the proper time to perform the operation, Enterprise faces yet another crisis. The ship, still stuck in the polaric field, is covered in nucleonic particles. The particles are continuing to accumulate and are having a negative effect on Enterprise — if the ship remains adrift much longer, every system will soon be off-line. Archer and the others are stumped, but Sim offers a solution: use the two shuttlepods (with some engine modifications) to "tow" Enterprise out of the field.

Archer agrees to Sim's plan, and initiates it from the bridge, with Mayweather and Reed piloting the shuttlecrafts. Just as their systems overload and it seems as if the plan is a failure, the shuttlepods manage to coax Enterprise into moving — Sim's plan is a success. Sim, however, is having some personal difficulties. For one, he has begun to have romantic feelings for T'Pol, and can't figure out if they're his own feelings or Trip's. Also, Phlox has some grim news: Sim will not survive the transplant.

Sim, however, believes that he knows of an experimental enzyme that will enable him to live beyond his 15 day lifespan. Phlox counters that there's no proof that the enzyme works. Besides, if Sim lives, Trip won't. Upset that his life seems to mean so little, Sim attempts to steal a shuttlepod and escape. He decides against it at the last minute, though. He tells Archer that he's realized his purpose in life is to help Trip, thereby helping Enterprise and all of Earth. Before he goes in for the operation, T'Pol bids him farewell, telling him that his absence will affect her and even giving him a good-bye kiss.

After Phlox successfully performs the operation, Archer conducts a funeral service for Sim, noting that the entire crew is grateful for the contributions he made in his short lifetime.