With the crew still reeling from Archer's supposed death while halting the launch of the Xindi Superweapon, T'Pol and the others determine that they now have somehow time traveled to the year 1944 during World War II. However, they also realize that discrepancies loom for the WWII they know and the current catastrophes taking place on Earth, particularly in the U.S., which seems to have been invaded by Nazis.
The captain is assaulted by Secret Service agents, including the sinister Ghrath – whom Archer suspects is an alien. Unbeknownst to Archer at the time, Ghrath is a subordinate of Vosk, an alien of Ghrath's race and a leader in league with the Nazis. Vosk is clearly troubled by Archer's appearance. With help from insurgents named Sal and Carmine, Archer is rescued from the agents, and taken to the apartment of Alicia, an African-American woman who soon realizes that Archer may be from another time and place. She convinces her friends Sal and Carmine to help Archer, as he tries piecing together this mysterious new situation. Archer incredulously realizes that Nazis have taken over the White House and nearly the entire Eastern seaboard during a disastrous new version of World War II.
On board Enterprise, the crew faces visitors of their own. First off, time traveler Daniels appears in horrific shape, giving details that the Temporal Cold War has become an all-out conflict with dozens of agents stationed throughout the timeline to wipe out others in a fight for complete dominance. He warns T'Pol and the others that they must stop "him" ... but doesn't give any names before he collapses.
While Trip works to repair Shuttlepod One, he is assaulted by the Suliban Silik, who escapes in the vessel. Believing that the "him? Daniels mentioned must be Silik, T'Pol sends Trip and Mayweather after him, which takes them to a U.S. locale near New York where Shuttlepod One has crashed.
Meanwhile, Vosk is intent on helping the Nazis force their reach — and their concentration camps — even further. Clearly, Vosk — who says he is in total agreement with the Nazis that their race must be "pure" — is receiving assistance from the Nazis in his own way and has convinced the Germans that they are all helping each other. Still, he is mysteriously obsessed with finding Archer, whom he regards as a threat to his mission.
Vosk's command to find Archer is successful as Ghrath tracks him down. During a fateful encounter with Archer, Ghrath reveals that his race is trapped and the Germans are helping them construct a conduit so they can return home. Ghrath also confuses Archer by referring to him as a "temporal agent.? Sal, trying to save Archer from Ghrath, kills him, convinced he is a Nazi who will only bring harm. Despite Archer's disappointment in seeing his information source muted, he absconds with a communicator that Ghrath had been holding. Shortly afterward, the menacing Vosk also finds Archer. But Archer — using Ghrath's communicator to call for a transport from a stunned Enterprise — escapes from him. Archer, with Alicia in tow, is transported back aboard where a relieved crew welcomes him home.
On Enterprise, Archer meets with Daniels, who is near death. Daniels explains that Vosk leads the most dangerous faction of the Cold War who is violently opposed to the Temporal Accords. When almost captured once before, Vosk had unfortunately developed a form of stealth time travel to escape into the past. This particular World War II time juncture provides the only point where Vosk can be stopped. When Archer reveals information he learned from Ghrath — that Vosk's faction is building a conduit — Daniels urges him to destroy it. Daniels knows the conduit's destruction will be the only way to stop Vosk from destroying all other races.
And just as Archer is getting this information — and Daniels trails off to his death — Vosk kidnaps Trip and Mayweather on Earth. With them in his grasp, Vosk hopes to get — and kill — the one impediment to his grand plan: Archer.
As the Nazi invasion of the U.S. continues in an altered 1944, Archer and his crew map out their strategy to stop Vosk from building a time machine that will take him back to his own time and inflame the Temporal Cold War, wreaking havoc upon the timeline. Having befriended American resistance fighters intent on battling the Nazis, Archer has a ready-made force on the ground to help with his cause.
But first, he is intent on bringing Tucker and Mayweather back on board Enterprise. Vosk hails Archer, offering the chance for a rendezvous to retrieve the two men, although the alien most certainly will expect some sort of recompense. Indeed, at the meeting, Vosk clearly needs the technology aboard Enterprise to accelerate his task in building the time machine. But Archer has no intention of helping him, though Vosk insists that he is changing the timeline for the better ... despite Daniels' ardent claims otherwise. Back on board Enterprise with Tucker and Mayweather, Archer and Phlox learn that Trip isn't actually himself: the Suliban Silik has taken on his identity. Upon his exposure, Silik reveals that he has left Vosk's compound with a disk that contains schematics and other information about the time machine. Determined now to retrieve Trip — who is trapped inside the compound — and armed with the new data, Archer heads back to Earth accompanied by Silik, who shapeshifts into human form. T'Pol is left in command with orders to take out the compound as soon as Archer deactivates the shields and he gives her the go-ahead from the surface.
With the help of resistance fighters Alicia and Carmine, Archer and Silik head into Vosk's compound to deactivate the machine which is soon to be completed. Meanwhile, Alicia, Carmine and their cohorts fend off Nazi soldiers working on behalf of Vosk. However, as Archer and Silik make inroads to the machine's shields, soldiers descend on them. In the ensuing battle, Silik is wounded and dies. Just as Archer bids a farewell to him, the real Trip appears, having earlier freed himself from incarceration.
As German planes hover to protect the facility on Vosk's orders, Archer and Trip are transported back to Enterprise. Once there, Enterprise must do battle against the planes above the Manhattan skyline. Just as Vosk is about to enter a time portal, Enterprise fires upon his compound and destroys it, annihilating Vosk in the process.
Once Vosk's plan is foiled, Daniels — alive once again — appears to Archer, showing him that the timeline is resetting itself, and that all the damage Vosk caused never happened.
Within moments, finally, Archer and his crew are back to their own time, on their way home after saving Earth from the Xindi superweapon.