Enterprise has been in the Delphic Expanse for six weeks and have yet to get any intel about the Xindi. Strange anomalies affect the ship, sending cargo flying violently through the bays, pockets of atmosphere losing gravity and other incidents defying the known laws of physics. T'Pol helps Trip's insomnia with an intimate Vulcan therapy. Archer and Trip find another race of Xindi imprisoned in a mine.

Enterprise follows a lead and discovers a Xindi lab that refines Kemocite, the key ingredient in the weapon being built to destroy Earth. An away team of Archer, Reed and Hayes confront the lead researcher, Gralik Durr, who was employed by Degra to refine the Kemocite but was never told what it would be used for. When Gralik realizes it was his research that contributed to the 7 million deaths on Earth, he agrees to help Archer prevent further loss of life. Meanwhile, on Enterprise, Phlox and Tucker study the weapon they seized from the Xindi and find an organic component, a life-form serving as the rifle's power cell. Despite T'Pol's objection, Tucker tests the weapon.

With Reed and Hayes fighting over a training program and Trip seemingly making T'Pol jealous, Enterprise discovers a dying alien in a pod with technology similar to the Spheres.

Captain Archer orders the crew of Enterprise to save a Xindi-Insectoid hatchery.

While the Reptilians force Hoshi to decipher a launch code, the Primates, Arboreals and Archer think of a way to stop the Xindi weapon.