Enterprise has finally reached Azati Prime, the site of the Xindi superweapon. Unfortunately, Reed can't find any weak spots in the Xindi's formidable detection grid. Archer suggests utilizing the Insectoid shuttle the crew recently salvaged to sneak past the grid and locate the weapon — perhaps they will be able to blend in. After learning how to operate the craft, Mayweather and Trip take it into Xindi territory, hoping to scan the weapon. They clear the detection grid and find that the planet is largely oceanic. They detect what could be the weapon, so they take the shuttle underwater. Once there, they find what they're looking for: the weapon is massive, a truly impressive and horrific sight. They take their scans and head back to the ship. Meanwhile, Enterprise is detected and scanned by a Xindi monitoring facility on the moon's surface. Archer, worried that the facility will alert the rest of the Xindi, is forced to destroy it.
With Trip and Mayweather safely back onboard, Archer studies their scans and hatches a bold plan. One crewmember will need to take the Insectoid craft, armed with torpedoes, back to the site of the weapon and blow it up. The trip, however, will be one-way, a suicide mission — and Archer wants to be the one to carry it out. The crew objects, but the captain's decision is final.
As he prepares for the mission, Archer is confronted by the mysterious time-traveling operative known as Daniels. This time, Daniels brings Archer four hundred years into the future to the Enterprise-J. Daniels illuminates the mystery behind the Expanse's sphere-builders. The sphere-builders are trans-dimensional beings — the test subject Enterprise recently encountered belonged to the same species. As Archer suspected, these beings are reshaping the Expanse to make it habitable for their species. It is, Daniels notes, a prelude to an invasion. In the future, the "Federation" Daniels keeps mentioning — which humans are an integral part of — drives these trans-dimensional beings back into their own realm. The beings, who are able to examine alternate timelines, have seen this future and are determined to change the outcome. They are the ones who convinced the Xindi that humanity needed to be destroyed. In fact, Daniels says, humans will one day protect the Xindi from the sphere-builders.
Daniels insists that Archer needs to contact the Xindi and come to a peaceful resolution — the captain must not sacrifice himself. Archer, however, is determined to carry out his plan. Daniels finally gives him a medal that belongs to a Xindi crewmember of the Enterprise-J. This, he hopes, will prove useful.
After bidding an emotional farewell to his crew, Archer heads down to Azati Prime. But when he arrives at the weapon site, the weapon is gone. Archer is discovered and taken prisoner. He is then tortured by the Xindi-Reptilians, who want him to reveal information about Earth vessels in the Expanse. The Reptilian commander threatens him, saying that they know where Enterprise is and can easily destroy it. Archer relents — but he will only talk to Degra, the Xindi-Humanoid Enterprise has encountered in the past. Using the information and the Xindi medal from Daniels, Archer attempts to convince Degra that deploying the superweapon will lead to the extinction of both their species. Archer is able to make inroads with Degra and some of Degra's Xindi allies, but the impatient Reptilian commander returns and orders Archer taken away for more questioning. He also reveals that Enterprise is under attack. Degra angrily insists the Reptilian call off the attack, but the Reptilian merely has Degra escorted back to his ship.
And indeed, Enterprise is weathering what may be the worst battle its crew has ever faced. The Xindi have managed to brutally damage the ship and the crew is valiantly struggling to stay alive...