Trip suffers a catastrophic injury in an accident that disables Enterprise inside a hazardous space cloud. His only hope for survival is a transplant from a clone or "mimetic symbiont" which Phlox grows from one of his exotic creatures. Phlox and the crew named the clone Sim. But his rapid growth and replication of Trip's behavior alarm the crew. Archer faces an ethical dilemma as the clone gains sentience and does not want to die from harvesting his organs for Trip's survival.

After Archer rescues them from their crippled vessel, the Triannons take the Enterprise crew hostage. These alien religious zealots plot to use the ship to eradicate heretics on their homeworld.