The Enterprise finally returns to Earth with great fanfare, and the weary crew members face repercussions of their journeys, both positive and negative. But the novelty quickly disappears for Archer, forced to vacation after a heated exchange with a Vulcan official. Also, Trip accompanies T'Pol to Vulcan, where he meets her mother, T'Les, but when T'Pol reconsiders marriage to her former fiance, Koss, Trip questions their relationship. The Xindi scare causes increased violent incidents against alien species on Earth, and Reed worries about Phlox's safety.

Cold Station 12 is a medical research facility where hundreds of genetically enhanced embryos left over from the Eugenics Wars are still stored. Arik Soong leads his band of Augments to the scientific outpost, intending to retrieve the embryos, bring them to life, and create a superhuman army of Augments. On the raid, Soong realizes just how ruthless his "children" have become and threatens to release the deadly pathogens stored on-site if anyone interferes.