Archer deals with the loss of many crew members and continues peaceful talks with two Xindi species that destroy a fellow Xindi ship in self-defense.
The Enterprise crew meet their descendants from an alternate timeline.
Archer speaks at the Xindi council and finds one species has launched the superweapon in defiance of the council.
Archer works to build support from the aquatic Xindi to stop the reptilians and find the Sphere Builders who are aiding the reptilians.
The final showdown with the reptilian Xindi to stop the weapon from destroying Earth. Archer is lost and believed dead as Enterprise finds itself back in the World War II era.
After destroying the Xindi weapon, Enterprise finds itself in the 20th century during World War II with Nazis in control of the North Eastern USA.
Archer joins Silik to stop the alien Nazis, restore the timeline and end the Temporal Cold War.
Enterprise is welcomed home after saving Earth and the crew takes a much needed vacation. Tucker & T'Pol visit Vulcan where T'Pol must consider marriage to Koss. Erika Hernandez becomes captain of the Columbia and renews her acquaintance with Archer. Phlox encounters prejudice on Earth.
Dr. Arik Soong restores his relationship with his genetically-enhanced "children," Augments.
A space station crew is held hostage as Dr. Arik Soong and his Augments work to obtain hundreds of Augment embryos in hopes of creating an Augment population.
Dr. Arik Soong finds himself overthrown as "father" of the Augments and Archer rushes to prevent the destruction of a Klingon colony. As a result of his dashed hopes of enhancing humans, Soong turns in a new direction of research.
Earth's embassy on Vulcan is partially destroyed by a bomb, killing Admiral Forrest. Archer & T'Pol travel to Vulcan in search of an alleged terrorist group blamed for the explosion, of which T'Pol's mother is a member.
Archer & T'Pol find T'Pau and T'Pol's mother and learn that Archer is carrying Surak's katra.
Archer and T'Pol bring back the Kir'Shara (Surak's artifact) that will lead to vast changes in the Vulcan world. T'Pol's Pa'nar Syndrome is cured by T'Pau.
Dr. Emory Erickson, inventor of the transporter, conducts a long-range experiment in order to recover his lost son.
Organians test the Enterprise crew by observing their reactions to a deadly silicon-based infection.
Andorians threaten war on the Tellarites after apparently being attacked by a Tellarite vessel en route to trade talks.
Archer and Shran engage in mortal combat as Archer tries to unite the Andorians and Tellarites who are being set at each other's throats by a remote-controlled Romulan vessel.
The drone Romulan ship that attacked the Andorians is under the control of an Aenar, an offshoot race of the Andorians. Archer and Shran join forces to rescue the Aenar and stop the Romulan plot.
Phlox is kidnapped by the Klingons who are seeking to cure a disease caused by an attempt to create Klingon/Augment hybrids; T'Pol's mental abilities grow after she conducts her first mind meld.
With the Columbia's help, the Enterprise crew grapples with sabotage to their ship as they pursue the truth behind the kidnapping of Phlox. The disease is cured, but genetic mutations will make many Klingons appear human-like for generations to come.
As a gift for negotiating with the Orion Syndicate, Archer receives three Orion Slave Girls, but these "gifts" have their own agenda. Meanwhile, Trip and T'Pol come to terms with the psychic bond that has been created between them.
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.