Archer and the NX-01 find themselves in Earth's past, with events of World War II altered by the Temporal Cold War.
With Silik's help, Archer hones in on the temporal operative who altered Earth's past and threatens to destroy all of time.
Once the NX-01 finally returns to Earth, the weary crewmen face repercussions of their journeys, both positive and negative.
When genetic supermen left over from the Eugenics Wars hijack a Klingon ship, Archer must rely on their creator, the criminal Dr. Arik Soong, to help hunt them down.
Arik Soong leads his band of Augments to a medical facility where hundreds of genetically enhanced embryos are still stored, intending to retrieve them and bring them to life.
In defiance of their "father," Arik Soong's Augments devise a heinous plot against the Klingons which will surely lead to interstellar war.
Earth's embassy on Vulcan is bombed, and the ensuing investigation puts Archer and T'Pol on the trail of a Vulcan religious faction hiding in a treacherous desert.
Archer and T'Pol encounter the Syrrannites, a radical group hiding in the Vulcan desert, while the NX-01 crew contends with Vulcan power ploys.
Archer, T'Pol and T'Pau attempt to bring the Kir'Shara — an artifact believed to contain Surak's original writings — to the Vulcan capital, as the NX-01 gets involved in a Vulcan-Andorian military clash.
The inventor of the transporter, Emory Erickson, comes aboard Enterprise for a risky experiment.
Non corporeal aliens study the Enterprise crew as they respond to a fatal viral infection brought on board from an away mission.
Enterprise journeys to Babel with a Tellarite ambassador on board for peace talks with the Andorians, when a distress call from Shran is received.
Archer tries to unify the Andorians, Tellarites and Vulcans in a plan to capture a marauder ship threatening to destabilize the region.
Archer visits Shran's icy homeworld to find an Andorian subspecies called the Aenar, to determine their connection to the marauder destroying ships in the region.
While Enterprise visits Earth for the launch of Columbia, Phlox is kidnapped and forced to help the Klingons deal with a grave threat toward their species.
With Columbia's help, the Enterprise crew grapples with sabotage to their ship as they pursue the truth behind the kidnapping of Phlox.
As a gift for negotiating with the Orion Syndicate, Captain Archer receives three Orion Slave Girls.
In the mirror universe, Commander Archer mutinies against Captain Forrest in order to capture a future Earth ship found in Tholian space.
In the mirror universe, Archer commandeers the 23rd-century Defiant from the Tholians and uses it in a nefarious power grab.
A xenophobic faction of humanity threatens to undermine talks to form a new coalition of planets.
A human isolationist leader threatens to destroy Starfleet Command unless all aliens leave Earth immediately.
Six years in the future, an emotional Captain Archer and the crew return to Earth to face the decommission of Enterprise and signing of the Federation charter.