Flanked by a flotilla of Primate, Aquatic and Arboreal ships, Enterprise enters Xindi space. Archer, Degra and a skittish Hoshi Sato head down to the Council chamber, located in an ancient stronghold built by the extinct Xindi-Avian race. Finally facing the Council, including the hostile Reptilians and Insectoids, Archer explains that the Sphere-Builders have manipulated the Xindi — they are really just preparing the Delphic Expanse for colonization. Someday, he says, Earth will lead a battle that will defeat the Sphere-Builders. They know this, and that's why they tricked the Xindi into attacking humanity. The Xindi-Primates, Arboreals and Aquatics seem open to Archer's findings, but the Reptilians and Insectoids refuse to believe him, claiming that Archer must have fabricated the data. As the debate grows more heated, the Council meeting dissolves into chaos.

Later, the Reptilian commander, Dolim, meets with one of the Sphere-Builders. The Sphere-Builder insists the Reptilians and Insectoids act together to secure the Weapon. This might mean civil war for the Xindi, Dolim points out. But the Sphere-Builder makes a guarantee that Reptilians will dominate the other Xindi species ... if they successfully deploy the Weapon and eradicate humankind.

Back on Enterprise, Archer and Degra work on their strategy. They need three of five votes to sway the Council, and Degra believes the key is to get the indecisive Aquatics on their side. The Aquatics respond to visuals more than words, so Degra cooks up a plan. Using data from Enterprise's encounter with one of the trans-dimensional beings, Degra constructs a biometric hologram of the being. The hologram effectively demonstrates the Sphere-Builders' previous presence on Enterprise. Intrigued, the Council is finally open to hearing more.

Meanwhile, T'Pol, Reed, Mayweather and MACO Corporal Hawkins are headed to a nearby Sphere in a shuttlepod. Hoping to gather more information on the Sphere-Builders, they plan to extract the Sphere's memory core. T'Pol discovers that part of the Sphere's surface is actually a hologram — the shuttlepod passes right through and T'Pol, Reed and Hawkins don their EV suits and head for the memory core. T'Pol manages to extract the memory core, but the Sphere has a spider-like defense mechanism that activates, putting the team in danger. They manage to fend it off, but Hawkins is killed during the fight.

On Enterprise, Degra approaches Archer with good news. Archer's presentation convinced the Council and they have the three votes they need! In fact, the Reptilians agreed to delay the deployment of the Weapon. Archer and Degra are overjoyed at this development, pleased that they've formed what seems to be a lasting alliance. Later on, however, Dolim approaches Degra in a room near the Council chamber. The Reptilian reveals that he knows about Degra destroying his scout ship. Degra tries to tell the commander that he had no choice, but Dolim won't listen — he stabs Degra.

Archer is devastated to learn of Degra's murder and the Reptilians' betrayal sparks further dissension among the Xindi Council. The Reptilians and Insectoids withdraw from the Council — they plan on stealing the Weapon and launching it after all. The Weapon, however, can only be launched with three of the necessary codes. The Reptilians and Insectoids only have two. But Dolim appears to have at least one more trick up his sleeve.

As the Insectoid and Reptilian ships prepare to steal the Weapon, they engage in battle with Enterprise and the other Xindi ships. Then, to Archer's horror, Hoshi is beamed off the bridge — the Reptilians have kidnapped her. And then the Weapon and escorting ships disappear into a vortex ...