The Enterprise crew hurries to avert disaster. John Frederick Paxton prepares to fire at the Starfleet Command complex by using their Verteron Array. While T'Pol and Trip are held hostages by Paxton, Paxton shows the Vulcan-Human hybrid baby. In the meantime, the crew of Enterprise devises a plan to camouflage the shuttle in a comet heading toward Mars' North Pole. Trip has to help Paxton to fix his weapons. When Trip is caught sabotaging the weapons, Paxton orders him into the detention center, from which he then escapes.
When Archer, Reed, Phlox, and Mayweather infiltrate the Orpheus Mining Complex, they find Trip and team up. They manage to get into the control room, where Josiah tries to prevent Trip from shutting down the array by shooting him. Josiah is also shot and a firefight ensues between Paxton and Archer. A phase pistol shot misses and hits the window, causing the room to start to depressurize, while reed is hit by another shot. While Archer puts his mask on Trip, Paxton speaks about Henry Archer and tells Captain Archer the reason why he turned against humanity. He says it was because Henry wanted the warp five engine badly. The window breaks and Paxton arms the weapon. The beam fires into the Pacific Ocean, not at San Francisco, due to Trip's intervention. After Paxton is arrested, the crew discovers that there is a Terra Prime operative on Enterprise. The crew scrambles to save Nathan Samuels from harm. When Archer finds the operative, the operative shoots himself.
Meanwhile, Dr. Phlox scrambles to find a cure for the baby, named Elizabeth by T'Pol, who is dying due to defects in the Terra Prime doctors' attempts to reconcile Human and Vulcan DNA. Unfortunately, Phlox is unable to save the girl; the leaders of the soon-to-be-incorporated Coalition of Planets later request to attend her funeral.
Later, Trip arrives in T'Pol's quarters; though they are both still mourning their devastating loss, Trip tells T'Pol that Phlox has determined that the flaws in the cloning process are correctable, and that in the future, Humans and Vulcans could choose to have children. In an ironic turn for the woman who refused to shake his hand when they first met, T'Pol takes the sobbing Trip's hand in hers as they sit together.