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His memory crippled, Archer awakens years in the future, after the Xindi have reduced Earth to a cinder and the remnants of humanity have settled on a distant planet. Now, Archer learns that he may be the key to undoing this tragedy.

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

On the first anniversary of her assignment to Enterprise, T'Pol tells Archer and Trip about the first contact between humans and Vulcans, which involves three Vulcans becoming stranded in the town of Carbon Creek, Pennsylvania in 1957.

While the Reptilians force Hoshi to decipher a launch code, the Primates, Arboreals and Archer think of a way to stop the Xindi weapon.

An Arctic research team makes a startling find: cybernetic creatures - Borg - buried in the ice. When the revived aliens seize control of a spacecraft, it's up to Archer to keep them from contacting the Collective and threatening Earth.

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.

Enterprise escorts Tellarites to peace talks with Andorians. While transporting they rescue Andorians and say the Tellarites attacked them. Enterprise is soon attacked by an Andorian ship, and Archer must prove who is responsible.

While Enterprise travels to Andoria to warn them of the attack, Archer tries to bring the Kir'Shara to the High Command.

Enterprise has found the location of the testing site of the Xindi weapon and gets some rather unexpected help.

Archer decides to make a fast-growing clone of Trip to help save his life while Enterprise is stranded in a dangerous field with nucleonic particles.

Enterprise has arrived at the location of the Xindi Council and with the help of Degra, Archer can make his plea in front of the five races of Xindi. Archer needs to prove that the Sphere Builders have been telling lies. While the Primates and Arboreals are already aware of the truth, convincing the other three races will not be easy. The Reptilians and Insectoids refuse to even listen to Archer. Meanwhile, the Sphere Builders haven't been sitting still, and have arranged a secret meeting with the Reptilians.

Captain Archer must convince Vulcans, Tellarites and Andorians to unite to find the Romulan ship.

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.

Set in the dark and oppressive Mirror Universe, Commander Archer leads a mutiny in a bold attempt to seize control of an advanced starship - a vessel from the future that may be the key to saving the Terran Empire.

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.

Enterprise finds out the marauder was piloted telepathically by an Aenar, a subspecies from Andoria.

An alien probe launches a devastating attack on Earth. Archer, still being hunted by the Klingons, brings the Enterprise back home to investigate.

After a bombing destroyed the Earth embassy on Vulcan, a group known as the Syrrannites are suspected. T'Pol receives a map from her Syrrannite mother, leading into a dangerous desert, the Forge.

Captain Archer has been returned to Enterprise by the Xindi council awaiting a hearing. But after a heavy attack by the Reptilians, Enterprise is stranded without a functional warp drive. They meet another ship in trouble because of space anomalies. The ship's captain isn't willing to trade in their warp coil and Archer must make a tough decision. Meanwhile T'Pol is having some strange sensations and can't control her emotions.

Enterprise discovers a pod with the body of a human that seems to be wanted by both Sulibans and Tholians.

The Mirror Universe saga concludes as Archer declares himself captain of a formidable starship from the future, while his alien crew launch a rebellion in a desperate bid to keep him from achieving ultimate power.

Archer and the Xindi Degra are in a shuttle. With Degra suffering from memory loss, Archer tells him they escaped together from a prison and that the Insectoids took power after destroying Earth.

Paxton threatens to destroy Starfleet Headquarters if all aliens don't leave Earth. Enterprise must shut down the verteron array on Mars, but it is extremely well defended.

T'Pol and Archer confront the Syrrannites and meet T'Pau who denies the embassy bombing. Archer, who has Surak's essence, is asked to help. V'Las threatens Enterprise to make sure an attack on the Syrrannites isn't witnessed.

Enterprise seeks repairs from their encounters with the Romulans, where they stop at a desolate but idyllic repair station. But all is not what it seems when Mayweather is suddenly found dead.