Moment after watching Enterprise's fiery explosion, Archer and his team are attempting to escape on the Defiant. The Tholian ships try to trap them with their deadly web, but Archer and crew manage to get the Defiant's systems working and use the ship to fight their way out. They also bring the escape pods from Enterprise onboard.
Archer and Hoshi peruse the ship's computer for information on their parallel universe counterparts. Archer is shocked to find no mention of the Empire — only something called "The United Federation of Planets." He's also disturbed to learn that his alternate universe counterpart is a starship captain and revered explorer.
The crew eventually discovers that they are not alone on the Defiant — a strange, reptilian creature known as a Gorn is hiding onboard, and he seems intent on sabotaging the ship. Archer goes after the Gorn and the two engage in an intense physical scuffle. Archer manages to get the upper hand by changing the gravity in that particular section of the ship and shoots the alien.
Later, the Defiant saves an imperial starship, the Avenger, from a rebel attack. Admiral Black, who is in command of the Avenger, is shocked to see Archer at the helm of this futuristic, alternate Earth vessel. Black tells Archer he will recommend him for a command as soon as possible, but Archer is impatient. Tormented by mocking visions of his more accomplished parallel universe counterpart, Archer becomes enraged. He's determined not to let Black take the Defiant from him. His megalomania and paranoia building, Archer shoots and kills Black. He then brings the Avenger's crew under his command and tells them that he plans to seize control of the Empire.
At least one person isn't sure of this plan, however . T'Pol believes that Archer will use the Defiant's advanced weapons to completely wipe out the rebellion, including thousands of Vulcans. She approaches Avenger crewmember Soval with a plan of her own — she wants to steal the data on Defiant's engines and tactical systems, give it to the rebels and destroy the ship. The duo manages to recruit Phlox and other non-Terrans to their cause.
T'Pol is found out and taken prisoner, but Soval manages to get control of the Avenger while Phlox sabotages the Defiant. It's all for naught, however — Phlox is taken down before he can complete his sabotage and the Defiant destroys the Avenger.
Later, onboard the Defiant, Archer and Hoshi celebrate. Archer plans to erase the ship's historical database, to prevent information getting out on the alternate universe. As Archer toasts his imminent reign as Emperor, he suddenly finds himself gasping for breath. He realizes that Hoshi has poisoned him. As Archer takes his final breaths, Hoshi reveals her co-conspirator: Mayweather. The two kiss passionately while Archer dies.
Now in command of the Defiant, Hoshi orders all to surrender to Empress Sato — the new ruler of the Terran Empire.