Aboard Degra's ship, Archer, Reed and Hoshi work with the Arboreals and Primates to stop the Xindi weapon from launching. Archer plans to destroy the weapon from the inside by overloading the power systems, but he needs Hoshi to decrypt the weapon schematics. A ragged Hoshi is still recovering from her ordeal with the Reptilians, but she's determined to help. Despite her condition, Archer plans to take her with him when he boards the weapon. As Archer outlines his plan, he suddenly finds himself transported to a futuristic council hall — he's face-to-face with Daniels, the mysterious time-traveling operative he's encountered many times before. Daniels tells Archer that he's going to be a crucial part of forming the "United Federation of Planets" that Daniels has spoken of before. He urges Archer not to go on this mission and to send Reed or someone else. Others are not crucial to the future of mankind — Archer is. Archer, however, won't be swayed. He's determined to complete the mission himself.
Meanwhile, T'Pol and the rest of the crew are taking Enterprise to Sphere 41. They hope to disable it and disrupt the entire Sphere network. The Sphere-Builders have been observing Enterprise, and set about transforming the space around Sphere 41. Phlox notes that entering this altered space will kill the entire crew — however, he can synthesize a compound that will protect the crew for 15 minutes, giving them just enough time to disable the Sphere. As they enter the dangerous area of space, Trip aims a deflector pulse at a specific point on the Sphere. Suddenly, several Sphere-Builders appear in Engineering and disrupt power. As the beings continue to interfere, Trip finds it difficult to maintain the pulse. Luckily, Phlox remembers a few details about trans-dimensional physiology, and tells the MACOs to alter their weapon frequency to compensate. They manage to hold the Sphere-Builders off long enough for Trip to restore the pulse and destroy the Sphere. As it implodes, it sets off a chain reaction, destroying the rest of the Sphere network. As they are no longer in altered space, the Sphere-Builders onboard Enterprise disintegrate.
Finally, Degra's ship reaches the Xindi weapon. The weapon is still being guarded by Commander Dolim's ship, and the Reptilian prepares to engage Degra's vessel in battle. Suddenly, help comes from an unlikely source: the Andorians, led by Commander Shran. The Andorian ship takes on the Reptilian vessel, proving to be more than a match for it. As the Andorians fire on the Reptilians, Shran tells Archer and the others to head for the weapon — and also manages to mention that Archer now owes him one. Archer, Hoshi, Reed and the MACOs transport to the weapon. While Reed and the MACOs fend off the Reptilians, Hoshi uses the data she's decrypted to help Archer overload the weapon. Once Archer is nearly finished with the job, he sends Reed, Hoshi and the others back to Degra's ship.
Just as Archer is completing his task, Dolim beams aboard the weapon and engages the captain in a brutal fight. Just as things look dire, Archer manages to plant one of his explosive charges on the Reptilian, blowing him up. Soon after, the weapon begins to overload. As explosions go off around him, Archer runs for safety. In a matter of seconds, the weapon is destroyed and Earth is saved ... but Archer's fate is uncertain.
Back on Enterprise, T'Pol and the others are waiting for Degra's vessel at the rendezvous point. They are pleased to find that many of the spatial anomalies in the area have vanished — the Expanse appears to be returning to normal space. Finally, Degra's ship arrives and Reed, Hoshi and the MACOs return to Enterprise. Archer, however, is not with them. Reed reveals that the captain did not survive the mission.
As the crew tries to absorb this devastating turn of events, T'Pol confers with the Xindi-Primate. He tells her that the Xindi Council has reconvened, and that the Reptilians will most likely join them eventually. Archer's sacrifice will not be forgotten.
After a long, difficult mission, the crew finally returns to Earth ... but Starfleet isn't responding to their hails. T'Pol sends Tucker and Mayweather down in a shuttlepod. As they reach San Francisco, they're greeted with a bizarre situation: they're being fired upon by a group of World War II-era planes!
Meanwhile, in a German hospital tent, a doctor is showing an injured man to a trio of Nazi officers. The man has been badly burned and is wearing a strange uniform ... it's Jonathan Archer! As the Nazi officers contemplate Archer, one of them emerges from the shadows. He's definitely not human ...