The Enterprise crew is back on Earth for an historic conference — humans, Vulcans, Andorians and other species have gathered together to form a coalition of planets. The conference is interrupted, however, when a disheveled woman bursts in and collapses to the ground. Before she dies, she presses a vial containing human hair into T'Pol's hand. Upon analyzing the hair, Phlox comes to a puzzling conclusion: it appears to belong to the offspring of Trip and T'Pol. T'Pol has never been pregnant, but she senses that what Phlox says is true: she and Trip have a daughter out there.
Hoping to get more information, Archer has Reed contact the mysterious covert operative Harris. Harris tells Reed that the woman who interrupted the conference, Susan Khouri, was a member of the underground xenophobic movement Terra Prime. Terra Prime's goal is to stop all human contact with alien species — they believe alien interference is corrupting humanity's way of life. Harris thinks Khouri was trying to leave the movement — and that her defection may have had something to do with Trip and T'Pol's child. He adds that Terra Prime is planning something, and the child may be involved somehow. If the Enterprise crew can find the child, they'll have the answers.
Thanks to clues from Susan Khouri's autopsy, the crew concludes that there may be a Terra Prime base in the mining colony of Orpheus, which is located on the moon. Trip and T'Pol go on an undercover mission to the colony, disguised as miners. Trip manages to infiltrate a Terra Prime meeting, but his cover is blown and he's taken prisoner. T'Pol is also captured, and the duo is brought before John Frederick Paxton, the leader of Terra Prime. Paxton, who is obviously passionate about his cause, is disgusted by Starfleet's attempts at friendly alien-human relations. He's determined to return Earth to its "rightful owners" — humanity.
On Enterprise, Mayweather has re-connected with an old flame, reporter Gannet Brooks. The two become romantically involved, but then Gannet is exposed as a spy for Terra Prime and thrown in the brig.
Meanwhile, Paxton orders the launch of the mining facility, which has been rigged to act as a very large ship. As Trip and T'Pol hang on for dear life, the facility lifts off the ground and goes to warp. With Enterprise in hot pursuit, the mining facility lands on Mars, near the planet's verteron array.
Paxton sends a subspace message on all frequencies. He declares that he's taken control of the Mars verteron array and can fire on any ship or facility in the system. As an example, Paxton fires on Earth's moon, gouging a large crater. Paxton says he won't use the weapon again, provided all non-humans leave the system immediately. Warming up to his zealous speech Paxton intones, "Terra Prime, forever?"