On the way to Azati Prime, Enterprise discovers a damaged Xindi-Insectoid vessel with no bio-signs onboard. Archer, Reed, Trip, T'Pol and Major Hayes board the vessel, hoping to learn more. They discover a pair of Insectoid corpses, a small assault vehicle and an eerie hatchery containing Xindi eggs, some of which are still viable. As the team explores the ship, Archer is suddenly spattered by a strange liquid that spews from one of the egg sacs.
Back on Enterprise, Phlox determines that Archer was hit by a mild neuro-toxin — most likely a defense mechanism. Later on, Trip reports that when the ship crashed, the Insectoid crew transferred their life support to the hatchery in an attempt to save their offspring. Hearing this, Archer orders Trip to assign a team to repair the hatchery — he notes that the Xindi want to destroy Earth because they think humans are ruthless. This would show them otherwise. Some crewmembers are puzzled by the captain's choice, but Archer stands firm. As time progresses, the captain's behavior becomes more erratic — he seems devastated by the death of one of the hatchlings, even going so far as ordering Hoshi to research Xindi burial rituals. When Trip tells him that the Xindi ship is in need of antimatter, Archer declares that Enterprise should transfer its antimatter to the vessel. He fervently insists that no more hatchlings are going to die.
This transfer, however, will severely deplete Enterprise's reserves and affect the crew's ability to carry out their mission. When T'Pol questions the captain's judgment, he relieves her of duty and confines her to quarters. Though Archer tries to brush off his increasingly strange decisions, Trip and the other officers can't help but be suspicious of Archer's obsession with the Insectoid eggs. Trip later manages to meet secretly with T'Pol to share his concerns.
Meanwhile, Reed, currently in command on the Bridge, encounters another Xindi-Insectoid vessel. The ship fires on Enterprise, but Reed manages to out-maneuver and destroy it. This infuriates Archer, who storms onto the Bridge and insists that the Xindi-Insectoids might have been able to care for the eggs. He stuns the crew by relieving Reed of duty and placing Major Hayes in command. He also asks Hoshi to transmit a distress call in the Insectoid language, a dangerous move that could very well put Enterprise in jeopardy.
As Archer prepares to head back to the hatchery, Trip and Phlox approach him and ask the captain to submit to a medical exam. Archer insists that it wait until he's back from the Xindi vessel. Given the captain's irrational behavior, Trip finally decides that it's time to take matters into his own hands. He, T'Pol, Reed and Phlox set out to stage a mutiny. While Trip and a crewman beam down to the Xindi ship to retrieve the captain, Reed, T'Pol and their team storm the Bridge. With help from Hoshi and Mayweather, they manage to wrest control from Hayes and the MACOs. Trip, meanwhile, has found the captain, who is treating the hatchlings with a bizarre maternal affection. Trip finally uses a phase-pistol to render the distracted Archer unconscious, and takes him back to Enterprise.
Back on the ship, Phlox finds an explanation for Archer's strange behavior. When the captain was sprayed by the egg sac, a neurochemical in the substance infiltrated his synaptic pathways, causing him to believe that he was the hatchlings' caretaker. Though Trip feels guilty about betraying the captain, Archer assures him that it was for the good of the mission. With the mystery solved, Enterprise resumes its course to Azati Prime.