The episode is about the non-corporeal aliens who secretly board the Enterprise to study its crew and their response to their fatal and viral infection brought on by the Enterprise as part of the aliens' mission.
Commander T'Pol, the Enterprise's doctor, assists the crew in the Sickbay. Captain Archer and T'Pol, and has provided assistance. Phlox, along with Hoshi, scan the infected crew of the pathogen compound.
As some of the crew are playing friendly games, it becomes more apparent that Mayweather and Reed are inhabited by the members of the alien species, with the intention to intrinsically observe the reaction of humans in handling and facing an imminent threat that could lead to tragedy or termination.
The scene becomes dreadful. The two, apparently, serve as the host bodies of two alien entities. Their conversation shifts to an imminent danger, one which has been encountered by space farers regarding dreadful infections.
As the Enterprise is recalling from the usual scavenger and expedition routine of a mysterious planet, Trip coughs heavily and collapses, as he experiences a sudden pain in his lungs. He could hardly breathe, making Hoshi navigate and fly their shuttle pod. She calls the Enterprise for an emergency landing. Abruptly, Hoshi also experiences dizziness and falls ill. Dr. Phlox, the medical officer of the ship, examines the two and later on delivers and declares his prognosis on the crew that Hoshi and Trip are infected with an incurable virus that is of silicon-based instead of one which is carbon-based and that it would remain unstable. If it will not be removed within hours, it will definitely kill them, including those whom they have come in contact with as it is regarded as highly contagious.
Hoping, that Hoshi and Trip would survive, Phlox injects them a sedative to ease the pain; it would cause them to temporarily drift off to sleep. Apparently, Trip and Hoshi are able to sit up from their bed; they are already inhabited with the aliens, providing them the chance to use their bodies and communicate with the other crewmembers. The aliens also wish to experience sensations of human emotions and the illness itself. Through a video link in the Sickbay, Phlox is stunned with Hoshi and Trip. They wake up and are able to speak profusely. While the two converse at each other, the doctor listens and compares their brain wave patterns with the base references. Phlox's fears are confirmed that both Hoshi and Trip's body are indeed inhabited by aliens. Phlox is shocked when the two aliens have admitted that they are still in the bodies of the two patients. Through telepathy, the aliens have sensed that their real identity have already been revealed so they confront the doctor and after a while, destroy the evidences that prove their presence. They immediately silenced Phlox through erasing his memory about the event as what they have done with Reed and Mayweather.
After the aliens have left Trip and Hoshi's bodies, Hoshi experiences cardiac arrest. Hoshi loses her vital signs and though wearing his bulky gloves, Phlox strives to fill an intra-cardiac syringe. Upon realising the situation, Phlox admits that he cannot handle it and asks T'Pol to conduct the defibrillator to Hoshi. Aside from T'Pol, Archer is also in the room, due to desperation Phlox tries to remove his gloves; however, Archie stops him and voluntarily removes his gloves and bio-hazard helmet; exposing himself to the deadly virus to revive Hoshi.
Thus with the stoic incident and situation, Archer has accepted his dreadful fate, making T'Pol as the commander of the Enterprise. Archer stays with Trip.
Although Trip has no alien inhabiting inside him, another alien dwells inside him. The first alien leaves a seed inside Trip; he sits up and confesses to Archer that he likes to use and occupy Trip's body to communicate and conduct research with the humans through experiments. Archer is furious after the aliens have admitted that it was them who have brought the deadly virus in the Enterprise, including the antidote and the power to heal or cure those who are infected.
Archer begs the aliens to help them cure the body of his best crew Hoshi and Trip. Archer's compassion wins in the end. The aliens bring Hoshi and Trip back on their feet. The aliens are impressed on the feelings and concern of the human through Archer. As a reward for Archer's compassion, the aliens give him the cure that could heal all the infected crew aboard the Enterprise. Then, they have left in peace.