After helping to repair the warp drive on board of a Xyrillian ship, Trip notices a strange bulging on his arm.

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 helps an alien woman, Rajiin, seeking to escape her life as a sex slave. Once on board she uses her alien abilities to gather biometric data about humans and is recaptured by her employers, the Xindi council.

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.

Enterprise has found the location of the testing site of the Xindi weapon and gets some rather unexpected help.

Archer and the Xindi Degra are in a shuttle. With Degra suffering from memory loss, Archer tells him they escaped together from a prison and that the Insectoids took power after destroying Earth.

Archer decides he should pilot a kamikaze shuttle to destroy the Xindi weapon. Temporal agent Daniels urges him to reconsider.

Captain Archer has been returned to Enterprise by the Xindi council awaiting a hearing. But after a heavy attack by the Reptilians, Enterprise is stranded without a functional warp drive. They meet another ship in trouble because of space anomalies. The ship's captain isn't willing to trade in their warp coil and Archer must make a tough decision. Meanwhile T'Pol is having some strange sensations and can't control her emotions.

As the crew continues to repair the ship and mourn the dead, Archer works to create trust and form a partnership with members of the Xindi council.

Trying to pass through a subspace corridor, Enterprise is stopped by a version of itself from the future.

Enterprise has arrived at the location of the Xindi Council and with the help of Degra, Archer can make his plea in front of the five races of Xindi. Archer needs to prove that the Sphere Builders have been telling lies. While the Primates and Arboreals are already aware of the truth, convincing the other three races will not be easy. The Reptilians and Insectoids refuse to even listen to Archer. Meanwhile, the Sphere Builders haven't been sitting still, and have arranged a secret meeting with the Reptilians.