Computer logs retrieved from the wreckage reveal the survivors cut off their own life support and suffocated in order to save the ship's hatchery. Despite Sub-commander T'Pol and Commander Tucker's objections to the delay in Enterprise's mission, Archer orders Tucker to return to the ship and repair the hatchery's bio-support. Incompatibilities with Enterprise portable power generators cause an overload, prematurely hatching one of the eggs. Archer conspicuously declares a medical emergency, but Phlox cannot save the organism.
At this point, Archer, who has been awake for several days, orders the transfer of one-third of Enterprise's antimatter supply to the Xindi ship so that its power can be restored. When T'Pol refuses to carry out his order in front of the crew, he relieves her of duty and confines her to quarters. Soon after, Lt. Reed, whom Archer put in control of the bridge, destroys a Xindi ship that shows up and attacks the Enterprise. Archer responds by relieving and confining him as well, saying that the ship and its crew could have been used to save the eggs in the hatchery.
Archer then stations MACOs throughout the ship and promotes Major Hayes to First Officer. Tucker and Phlox covertly perform a medical scan of Archer, hoping to find a medical reason to declare him unfit for duty, but it reveals nothing. Leaving Hayes in control of the ship, Archer takes the anti-matter down to restore the Hatchery's bio-support power. Despite the scan results, Tucker decides that a mutiny is in order, and they free T'Pol and Reed to assist in the task. After a tense standoff with the MACOs which ends when Ensign Mayweather tackles Hayes, the Enterprise crew capture the bridge and Hayes gives up command. Meanwhile, Tucker beams down to the hatchery and stuns Archer.
Back on Enterprise, a thorough medical scan by Phlox reveals that the eggs had sprayed Archer with a substance that led him to believe he was their caretaker. As such, he became focused on preserving them and ensuring their safe hatching. In the end, Archer is returned to normal and a large number of the eggs survive.