Enterprise has a group of aliens watching a stellar phenomenon on board. When the ship is miraculously saved from blowing up, crewman Daniels has an important message for Archer.

Enterprise discovers a mining colony of the Paraagans. The crew gets an invitation for a meeting on the surface and a shuttle pod tries to break through the atmosphere. All of a sudden just under the shuttle a giant explosion begins and scorches the earth beneath. All 3600 colonists are reported dead. After examination, Enterprise finds out plasma leaking from the pod's vents ignited tetrazine in the atmosphere. Lieutenant Reed, however, ensures he closed the plasma vents before the shuttle went of. After conversations with admiral Forrest of Starfleet Command, Captain Archer learns that Enterprise's mission is canceled and they must return home, not to return to space for another ten or twenty years. When the ship has altered course, crewman Daniels, a time traveler, pays a visit to captain Archer.

Captain Archer and temporal agent Daniels have been stranded in the 31st century. In a library they investigate the damage to the time line and try to find way a to get Archer back in his own century. Meanwhile Silik the Suliban leader is trying his utmost to find the whereabouts of Archer and he is willing to go far for the answer. But the crew of Enterprise has plans of their own. Trip finds a way to use the com system and is able to speak with Reed. Together they try to contact other crew members and make plans to purge Enterprise of the Sulibans.

Archer and T'Pol travel back in time to Detroit in 2004 to stop three Xindi-Reptilians from constructing a bioweapon.

Archer decides he should pilot a kamikaze shuttle to destroy the Xindi weapon. Temporal agent Daniels urges him to reconsider.

Archer takes Degra's ship to try to prevent Earth from being destroyed and gets some unexpected help. Enterprise tries to destroy Sphere 41, but the Sphere Builders know about the plan.

Following the destruction of the Xindi weapon, the Enterprise crew discovers that they have been sent back in time to 1944. However, history has been altered, leaving Nazi Germany in control of a large portion of the eastern United States.

After Silik attacks Trip, Vosk wants to make a deal with Archer: supplies of the ship for the completion of his time machine in return for a trip to the 22nd Century.