Having mysteriously survived the destruction of the Xindi superweapon, a battered Archer awakes to find himself back on Earth in the 1940s in the custody of Nazi SS agents, and learns that Nazi-uniformed aliens have successfully helped Germany invade the United States. When he manages to break free of his captors, Archer joins forces with American resistance fighters to unravel the conspiracy behind the occupation.
Meanwhile, believing Archer sacrificed himself to save Earth, T'Pol and the battle-weary Enterprise crew attempt to figure out how to return to their own time. But then a near-dead Daniels appears and informs them that the future has been wiped out by a faction of the Temporal Cold War, the same faction responsible for the altered events on Earth, and they must be stopped.
Seizoen 4
Archer reunites with his astonished Enterprise crew and learns from Daniels on his deathbed that a radical Temporal Cold War faction threatens to obliterate the timeline. Archer returns to the Nazi-occupied eastern United States of the 1940s, and enlists the help of resistance fighters Alicia Travers and Carmine to destroy a massive time machine under construction on the surface.
Meanwhile, hoping to forge an alliance with Archer, alien leader Vosk releases his captured prisoners Tucker and Mayweather, but this forces temporal agent Silik to emerge from the shadows to pursue his own agenda against Vosk.
As the Enterprise crew revels in a heroes' welcome on Earth, Trip joins T'Pol on a trip to planet Vulcan, excited to visit her home and be introduced to her mother T'Les. But when T'Pol becomes obliged to reconsider marriage to former fianc? Koss, the future of their relationship is put in question. Meanwhile, Archer must defend some of his morally questionable decisions during the Xindi conflict before a Starfleet Command panel of inquiry. Later, Phlox experiences prejudice against aliens while taking shore leave on Earth with Malcolm and Travis.
After a dangerous group of genetically engineered humans called "Augments" escapes from their secluded planet intent on causing all-out war between Earth and the Klingons, the Enterprise crew is called into action and Archer enlists the help of criminal genius Dr. Arik Soong, the scientist responsible for creating the Augments.
While searching for the Augments in the Borderland ? the volatile region between the Klingon Empire and the Orion Syndicate ? Enterprise crosses paths with a band of ruthless Orion slave traders, who kidnap T'Pol and eight other crew members off the ship so they can be sold at auction, forcing Archer to enact a risky rescue mission with Dr. Soong's help.
Reunited with his genetically engineered creations called Augments, criminal scientist Dr. Arik Soong and his "children" break into the medical outpost where Soong once worked, to steal the embryos of hundreds more potential Augments with plans to build a superhuman army. They will go so far as to release the deadly pathogens stored at the facility, Cold Station 12, if the staff, headed by Dr. Jeremy Lucas, dares impede Soong's plan. Meanwhile, Archer and his crew search for clues to Dr. Soong's whereabouts on Trialas IV, the planet where he raised the Augments, leading them to find one of the doctor's less perfect children who was abandoned by his siblings.
Enterprise pursues Arik Soong and his Augments across hostile Klingon space toward a planet where the geneticist intends to go back into isolation and raise an army of genetically engineered superhumans. But Soong's "children" revolt against him and plan a biological attack upon a Klingon colony, in order to incite retaliation against Earth.
The Earth embassy on Vulcan is bombed, killing 31 humans and 12 Vulcans. Enterprise is called to the planet to help investigate, but the Vulcan High Command already suspects a dissident religious faction known as "Syrrannites." T'Pol learns from her husband Koss that her mother T'Les has been forced into hiding to avoid arrest ? because she is a Syrrannite. Koss also brings her a mysterious heirloom containing a map. Believing this is a message from T'Les, T'Pol and Archer set out to follow that map across a treacherous desert, without the High Command's knowledge.
On a quest to learn the truth behind the bombing of the Earth embassy on Vulcan, Archer and T'Pol track down the Syrrannites, a revolutionary faction hiding in a desert sanctuary which includes T'Pau ? the prime suspect in the bombing ? and T'Pol's mother T'Les. The rebels are on the verge of being crushed by Vulcan High Command leader V'Las, but they are stunned to learn that Archer might hold the key to their survival.
While Vulcan's state of unrest grows more violent, former Ambassador Soval reveals to Trip that the High Command also plans to launch a massive sneak attack against rival planet Andoria, an act that could pull Earth into interplanetary war.
Archer, T'Pol and rebel leader T'Pau struggle to reach the Vulcan capital to publicly unveil their discovery of a revered ancient artifact that could revolutionize Vulcan society and topple the corrupt government.
Meanwhile, with help from allies among the Vulcans and Andorians, the Enterprise crew attempts to stop V'Las and the Vulcan High Command from launching a sneak attack upon rival planet Andoria.
The crew welcomes aboard Emory Erickson, the inventor of the transporter device, set to conduct a series of experiments to test a radical upgrade to the technology. However, once Enterprise reaches the test site, Archer realizes that his old family friend has lied and is using the ship to search for his son, lost years before in a transporter mishap.
After Hoshi and Trip contract a deadly virus while exploring a planet, two ghostly aliens possess the bodies of various Enterprise crew members to observe humanity's reaction to imminent tragedy. As the aliens secretly jump bodies to observe, Phlox strives to cure the stricken pair, but with his efforts failing, Archer must make a difficult decision in order to shield the rest of the crew from this growing biohazard.
Ordered to transport a delegation of argumentative Tellarites to a peace conference with the blue-skinned Andorians, Archer and the crew find themselves drawn into a confusing, dangerous situation when a secret Romulan vessel begins attacking ships on all sides, including Enterprise.
Trapped aboard a mysterious drone ship that's been terrorizing the region, Trip and Malcolm work to outwit the Romulans, who are piloting the vessel via remote control, in order to save their own lives and stop the feuding Andorians and Tellarites from going to war.
Andorian Commander Shran leads Archer to his frozen homeworld in search of the Aenar, a hidden, peace-loving race with tremendous psychic abilities, after discovering that one of the mysterious telepaths has been working with Romulans.
Meanwhile, Trip and T?Pol attempt to construct a device that will render the Romulans' remote-controlled ship useless and stop their swath of destruction in the region. Later, weary of the continuing friction with T'Pol, Trip comes to a surprising decision.
On Earth, Dr. Phlox is kidnapped by a band of Klingons who are desperate to find a cure for a genetically-engineered virus that threatens their entire race. Meanwhile, Trip begins his new assignment aboard the Starship Columbia as it prepares to embark on its maiden voyage.
But Reed's ties to a mysterious intelligence organization compromises his allegiance to Archer and Enterprise. Later, T'Pol attempts her first mind-meld in the search for clues to Phlox's whereabouts.
With the help of Captain Hernandez, Trip and the newly-launched starship Columbia, Archer pursues the kidnapped Phlox deep into Klingon territory, as Phlox decides to cooperate with finding a cure to a virus ravaging a Klingon outpost.
Meanwhile, Archer demands that Reed disclose his secret orders when his ties to a mysterious intelligence organization are revealed. Later, when Trip temporarily returns to Enterprise, T'Pol tries to broach an uncomfortable subject with him.
After Archer forges a deal with the Orions, the trader presents the captain with a gift -- three alluring Orion women who proceed to seduce all the men on board except, mysteriously, Trip.
In an alternate universe, an amoral, imperialistic version of the Enterprise crew, led by Captain Forrest with Archer as his treacherous first officer, makes an astonishing discovery during a mission into enemy alien territory.
While a power-hungry Archer schemes against Captain Forrest, his lover Hoshi, and loyal slave T'Pol, so he can lay full claim to the discovery. Later, Phlox happily tortures a captured Tholian for information requested by Archer.
After using the Defiant to repel a Tholian attack, the power-hungry Archer and Enterprise crew set about using this advanced ship to seize control of all of Earth's Terran Empire. As Archer takes full command of the Defiant and reviews the alternate history of Starfleet, his duplicitous lover Hoshi, a traitorous T'Pol and a reptilian Gorn stowaway hatch schemes of their own.
On Earth for a historic Starfleet conference to ratify the coalition of planets, Archer and the crew uncover a plot by a radical xenophobic group of humans called Terra Prime, led by Paxton, who want to put an end to the increasing number and influence of aliens on Earth. Meanwhile, although T'Pol contends she has never been pregnant, she and Trip learn that Terra Prime has information about their child. Later, a female reporter from Travis' past pursues him for a story.
In the first steps towards the foundation of the Federation, Captain Archer and the crew must stop Paxton, a well-armed, radical human isolationist leader, who is threatening 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, ratifying the newly-formed alliance of planets they helped forge.