After the crew learned about the supposed death of Captain Archer, they arrive home only to realise that they have somehow travelled back in time to the year 1944, in the middle of World War II. What's even more shocking is the Nazis seem to have invaded the eastern front of the United States and is on the brink of taking total control of the entire world... with some help from an alien species.
Under Daniel's request, Archer and his crew must stop Vosk from completing his time machine that will enable him to go back to his time and successfully changing the time-line to his favour. With some help from an old friend, Silik, and the American resistance fighters, the crew tries to destroy the time machine before it's too late and return to their original time-line.
The Enterprise finally return home after their year long mission in Delphic Expanse. While everyone is gracious of their successful mission, Captain Archer is particularly anguished in losing 27 crew members during the mission. At the Command Council, Ambassador Soval accused Archer that he didn't do enough to saved the Vulcan ship he found in The Expanse. Admiral Forrest sees the need for Archer to have some relaxation time and orders him to take a shore leave before he leave on his next mission. A reluctant Archer decides to climb mountains to clear his head, but soon finds an old friend from his days at the command school comes and joins him.
Meanwhile T'Pol decides to visit her mother back in Vulcan and invites Trip to join her.
When a group of super-humans invade and take control of a Klingon Bird-of-Prey, the Klingons want retaliation. Starfleet orders Captain Archer and his crew to take the Enterprise and retrieve the Klingon ship before any more damage can be done. The crew takes Dr. Arik Soong, a prisoner of Starfleet because he stole the embryos to create these super-humans, aboard, to help find the Bird-of-Prey. But along the way, the crew comes under attack by the Orion, who capture T'Pol and several crew members as slaves. Archer must go to the slave market and rescue his crewmen before it's too late, and Dr. Soong is the only person that can help them get in.
After a group of superhumans, the Augments, force their way into the ship and rescued their "father", Dr. Arik Soong, they are now on their way to Cold Station 12 to "awaken" thousands of other genetically-altered embryos of their kind. If successful, this group of superhumans will take over humanity. Captain Archer must figure out a way to stop them and rescue the hostages taken on Cold Station 12. However, this mission may end up taking his life, as a deadly pathogen is released inside the station.
With a deadly pathogen about to be released, Captain Archer barely makes it back to the Enterprise. His goal is now to track down the Klingon Bird-of-Prey and stop Dr. Arik Soong and the Augments from finding a location to raise thousands of Augment embryos.
Back in the Bird-of-Prey, Malik starts to question Dr. Soong's judgment when Soong wants to change the embryos' DNA to make them less unhappy and more human. Malik defies Soong's orders and takes leadership of the Augments. His goal is to create a war between the Humans and Klingon which would enable the Augments to grow in power. Soong realises his place is no longer with the Augments, and seeks to find an escape route off of the Bird-of-Prey. He realises that the only way he can stop Malik's plan is to join forces with Captain Archer.
A tragic incident shakes human-Vulcan relations to the core when a bomb is set off in a protected area of the United Earth Embassy that claims 43 lives, including that of Admiral Forrest. The bomb detonated just before the High Command may have been announcing its intent to conduct joint missions with Starfleet. In the throes of the blast, Forrest actually saved the life of an extremely grateful Soval. As Enterprise is called to Vulcan after the tragedy, Soval comes aboard the ship with the head of the Vulcan High Command, Administrator V'Las, and his security chief, Stel. With the embassy officially on Earth soil, Captain Jonathan Archer is to handle the official investigation. The initial research from the bomb fragments that Mayweather and Reed extricate finds the DNA fingerprint of a Vulcan, T'Pau. She is a member of the Syrrannites, a zealous Vulcan sect that believes in - among other Vulcan taboos - the practice of mind-melding. Syrrannites follow a corrupted form of the teachings of Surak, the father of Vulcan logic who is considered the most important Vulcan who ever lived. A wanted man named Syrran is the sect's current leader. With a Syrrannite now suspected, V'Las announces that Vulcans will take over the investigation.
As Captain Jonathan Archer and T'Pol reach the Syrrannite compound after crossing the treacherous Forge expanse, they are immediately treated like traitors. But as T'Pol's mom T'Les comes forward, the Syrrannite de facto leader T'Pau backs off a bit, especially after she realizes a dangerous exchange has taken place. Before he died, the Syrrannites revered leader Syrran mind-melded with Archer, giving the captain his "katra.? The Syrrannites regard the "katra? as the living spirit of Surak, a man who died 2,000 years ago and is considered the greatest Vulcan who ever lived. Archer, who has been feeling strangely since Syrran mind-melded with him, is having visions of Surak, and realizes that the notions of katra must be true. Further, while T'Pau tries to extract the katra from Archer through another type of mind-meld, Surak resists, staying firmly planted in Archer's consciousness. Surak has decided that Archer should have this katra; Vulcans cannot possibly understand the severity of dangers they currently face. In trying to protect Vulcans, Surak believes that Archer is his best recourse in saving his race.
The Vulcans having decimated the Syrrannite compound, Archer - with T'Pol and T'Pau - is driven on bringing the Kir'Shara relic to the Vulcan High Command. V'Las has succeeded in convincing his fellow High Command members that the Andorians will be using Xindi technology to obliterate the Vulcans - although they have a peace accord in place - and is plotting the attack. Because the future-knowing Surak is literally in his mind, Archer knows that time is of the essence; he must bring the Kir'Shara to the High Command before the Vulcans go to war with the Andorians. Unfortunately for Archer and his traveling companions, V'Las is going to extremes to thwart any interference they may cause in carrying out his battle strategy. Further, their showing up and professing the pacifistic views of the Vulcan Syrrannite faction would nullify his framing them for the embassy bombing. To that end, he has sent his henchman Talok to find Archer, T'Pol and T'Pau and "eradicate? them.
Captain Archer is delighted to welcome his mentor, Emory Erickson, who invented the transporter, along with his daughter, Danica, aboard Enterprise to conduct experiments in sub-quantum teleportation. Erickson seems to be progressing nicely in his work, until the ship enters the blackest and most dangerous area in space known as The Barrens, and a member of Starfleet is brutally killed by an amorphous shape.
While playing a friendly game of chess, it becomes apparent that Reed and Mayweather have been inhabited by two members of an alien species who intend to observe how humans react when faced with an imminent tragedy.
The Enterprise crew welcomes aboard a group of Tellarites, including Ambassador Gral, to transport them to the neutral planet of Babel, where Earth mediators will try to settle a long-standing trade dispute between the Tellarites and the Andorians. After receiving fragments of a distress call, Enterprise alters course to provide assistance, and arrive to find that an Andorian vessel has been destroyed by what seems to be a Tellarite ship. Though furious with the Tellarites for compromising the conference, Archer has no choice but to bring the Andorian survivors, including Commander Shran, aboard Enterprise.
Nijil and Valdore continue to control the mysterious Romulan ship that has trapped Reed and Trip, masking it to look like Enterprise and using the ship to destroy a Rigellian vessel. After a Romulan Senator named Vrax chastises Nijil and Valdore for losing control of the ship, Nijil and Valdore vow to hug the humans onboard (Trip and Reed) in order to cover their tracks. Nijil and Valdore trap Trip inside the service junction and leak radiation coolant inside. Over a speaker, Valdore orders Trip to re-establish the damaged warp matrix on the ship or he will die. Reed works frantically to free Trip, but the situation is made worse when the ship engages Enterprise in an intense firefight.
In the Romulan command center, Senator Vrax admonishes Valdore for the defeat of the drone ship. Vrax is also angry that the Andorians and Tellarites have formed an alliance. Valdore tells Vrax it is all merely a setback. Valdore plans to deal with the humans who brought the Andorians and Tellarites together - he has a second drone armed and ready and is prepared to use the two ships to find Enterprise and destroy it.
Enterprise has returned to Earth for the launch of the Columbia. While Trip prepares for his transfer, Hoshi and Phlox enjoy dinner in San Francisco. Things turn sour, however, when Phlox is kidnapped by mysterious aliens and taken to a Klingon laboratory on the colony world of Qu'Vat. Dr. Antaak and General K'Vagh inform him that a virus is spreading through the Klingon Empire - they need Phlox's help to devise a cure.
In Enterprise's brig, Archer briefs Reed on the situation: the Klingons altered the ship's engineering subroutines and if Enterprise drops below warp 5, the reactor will explode. Archer has a plan to bring Trip aboard from Columbia, but he needs Reed's help.
En route to a potential site for the first in a series of Starbases, Enterprise is hailed by an Orion ship. The ship's commander, Harrad-Sar, has a proposal to make: he claims to know of a planet with large deposits of magnesite and says he will give Archer the coordinates in exchange for a share of the profits. He also agrees to open a dialogue between Starfleet and the Orion Syndicate. To celebrate their new partnership, Harrad-Sar presents Archer with a gift: three Orion slave girls.
In an alternate universe, where the universe is ruled by the imperialistic Terran Empire, Commander Archer is the first officer of the I.S.S. Enterprise, serving under Captain Forrest. Archer wants Forrest to take the ship into Tholian space, where there may be a ship that can provide valuable technology to the Empire. But Forrest rejects his idea, thinking Archer is only trying to gain power. The determined Archer does not give up and recruits Major Reed and Sergeant Mayweather to stage a mutiny. Archer not only wants control of the ship, but also wants Forrest's lover, Hoshi, and hopes this mission in finding this ship can lead to him gaining more power in the Empire.
January 18, 2155: With the Enterprise destroyed, Archer and his crew decide to steal the Defiant and get out of the Tholian space station. The Tholian tries to trap them, but was no match for the advance technology of the Defiant. When Archer and his crew save an imperial ship of the Empire commanded by Admiral Black, Black wants Archer to surrender his ship to the Empire, but will give him another starship as soon as possible. But Archer doesn't want another ship, he wants the Defiant and will do anything that is neccessary to keep control of the ship and gain power in the Empire.
January 19, 2155: The Enterprise crew is back on Earth for an historic conference - humans, Vulcans, Andorians, Tellarites and other species have gathered together to form a coalition of planets. The conference is interrupted, however, when a disheveled woman bursts in and collapses to the ground. Before she dies, she presses a vial containing human hair into T'Pol's hand. Upon analysing the hair, Phlox comes to a puzzling conclusion: it appears to belong to the offspring of Trip and T'Pol. T'Pol has never been pregnant, but she senses that what Phlox says is true: she and Trip have a daughter out there.
As Paxton continues to deliver his xenophobic address, Enterprise's crew and the delegates assembled at Starfleet Command watch the broadcast in horror. Paxton shows an image of a half-Vulcan, half-human child - Trip and T'Pol's baby - as an example of how humanity's genetic pool will be diluted if alien-human relations continue. He notes that for the next 24 hours, he will guarantee safe passage for all aliens leaving the system. If any non-humans remain in the system after the deadline, Paxton will not hesitate to use the verteron array, and he will starts by blowing up Starfleet Command. As the Enterprise crew works furiously to block Paxton's transmission, they suddenly find their ship being targeted by the array. They manage to bid a hasty escape just as Enterprise is about to be destroyed.
About 200 years in the future, Commander William Riker of the starship Enterprise NCC-1701-D looks back at a historical event in the holodeck, hoping it will help him make an important decision...
It's been ten years since the Enterprise NX-01 was launched on it's maiden voyage and the crew now head back to Earth for the decommission of the ship and Captain Archer is about to deliver his speech in the historic signing of the Federation charter. But all good things doesn't come to an end until the crew embark on a final and dangerous mission to save Shran's daughter and one of their own will make a daunting sacrifice.