The Xindi-Reptilians have kidnapped Hoshi, hoping that she will be able to decipher the Aquatics' launch code. This will give them the three codes they need to deploy the superweapon and destroy Earth. Hoshi refuses to cooperate, so Commander Dolim has her injected with parasites that invade her neocortex and render her more compliant.
Meanwhile, Archer meets with Trip and T'Pol to go over strategy. Using the memory core that T'Pol retrieved from one of the Spheres, they determine that four of the dozens of Spheres are integral to the subspace energy grid that connects them all. The closest is Sphere 41 — if they can damage it, it might disrupt the entire grid, putting the Sphere-Builders' plans in jeopardy. Archer knows that time is of the essence — Enterprise needs to stop the Reptilians and Insectoids from launching the weapon. The Primates and Arboreals are already on his side, but he needs more firepower. With his Xindi allies by his side, Archer makes a plea to the leaders of the Xindi-Aquatics: help Enterprise stop the Reptilians, and he will disable the Spheres. After all, the Spheres are turning the Expanse into a trans-dimensional wasteland — unless they are destroyed, the Xindi will not survive. After much deliberation, the Aquatics finally agree to assist Enterprise.
Meanwhile, on the Reptilian ship, the parasites that were injected into Hoshi have done their job and she has decrypted the third launch code. Triumphant, the Reptilians prepare to arm the weapon. On Enterprise, MACO leader Major Hayes assembles a boarding party to rescue Hoshi. Reed discusses the plan with Hayes, and shares that he regrets he was unable to save Corporal Hawkins, who died while under his command. Hayes, however, knows that Reed did all he could. He assures Reed that his team will bring Hoshi back safe and sound.
Flanked by Aquatic, Arboreal and Primate vessels, Enterprise is finally ready to take on the Reptilians and Insectoids. As they engage in battle, Hayes and the MACOs transport to Dolim's vessel to rescue Hoshi. They manage to locate her, but there's a problem with Enterprise's transporter, and the team must be beamed out only two at a time. Hayes is the last to go and he's fatally shot right before he's beamed back. As a devastated Reed looks on, Hayes dies in Sickbay.
As the fight rages on, the Sphere-Builders observe from their trans-dimensional realm. Noting that the weapon is about to be destroyed, they use one of the Spheres to create a barrier of anomalies around the weapon. The Enterprise crew tries to penetrate the barrier, but the Reptilians manage to arm the weapon and enter a subspace vortex. They're headed for Earth. Inside the vortex, the Insectoid captain hails Commander Dolim. After observing how the anomalies worked to their advantage, he can't help but be suspicious that Archer's claims are true — that the Xindi "Guardians" control the Spheres and are merely manipulating the Xindi. Sensing dissension in the ranks, Dolim destroys the Insectoid ship.
Back on Enterprise, Archer must develop another plan. Since Degra's old ship is the only vessel that will be able to catch up with the Reptilians in time, the Xindi-Primates will take Archer, Reed and a team from Enterprise to the weapon. Once there, the team will board the weapon and disable it from the inside. Archer knows that he must also take Hoshi with him, as only she can decipher the encrypted schematics for the weapon. The ensign is in no shape to go anywhere after her ordeal, but Archer believes it's the only way.
Archer and company board Degra's ship, while T'Pol and Trip prepare to lead Enterprise toward Sphere 41 and disable it. As the two teams head off on their respective missions, the senior officers wish each other luck. Both plans must go off without a hitch.