Season 2 begins where Season 1 left off as Captain Jonathan Archer is trapped in the 31st century. During Season 2, Archer has numerous conflicts with the Vulcan High Command.
Daniels and Archer must find a way back to the 22nd Century in order to make sure history plays out as it should.
After Archer and Trip become curious about a visit T'Pol made to a Pennsylvanian mining town called Carbon Creek, she tells the two a tale about a Vulcan ship that crash-landed in 1957.
Whilst attempting to explore a new planet, Enterprise triggers a cloaked mine. While the crew deal with the resulting damage, it's discovered that another mine is stuck to the hull.
Suffering from damage inflicted in the Romulan minefield and unable to complete repairs on their own, Archer orders a distress call to be put out. A response leads Enterprise to a repair station, which surprisingly has no crew aboard it and is run by computer
Archer spends a night in sickbay after Porthos falls ill with a deadly virus following a visit to an alien planet.
In need of fuel, Enterprise visits a mining colony for deuterium supplies. The crew discovers that the colony is being controlled by Klingon marauders who are regularly pillaging the mined deuterium.
After T'Pol is contacted by the Vulcan High Command, Archer, Mayweather and T'Pol travel to an arctic world to apprehend a fugitive. The mission takes a dangerous turn when T'Pol begins to have flashbacks that suggest the events she remembers about a former mission may not accurately relate to what happened.
Archer and Reed return to a pre-warp society that is on the verge of war to recover a lost communicator.
While Enterprise is surveying a black hole in a trinary star system, the stellar phenomenon causes strange effects on the crew.
Hoshi experiences her first transporter experience and strange after-effects lead her to believe she wasn't reassembled correctly.
Trip boards an alien cargo vessel to help repair a stasis pod, which holds a beautiful woman in suspended animation. When the woman accidentally wakes up, she reveals she's not a passenger, but a prisoner.
When a lethal neutronic storm approaches faster than Enterprise can escape, the crew take shelter in the maintenance shafts inside the warp nacelles. They also provide refuge to a group of aliens, who aren't exactly honest about themselves.
During a solo test mission on Shuttlepod 1, Trip is attacked by a territorial alien and forced to land on the night side of a moon. As he tries to contact Enterprise, he discovers his alien foe has made an emergency landing nearby.
Enterprise visits a planet where an Interspecies Medical Exchange conference is being held. Dr. Phlox tries to obtain research on a terminal disease from the Vulcan contingency, without revealing T'Pol has been infected by it.
Both the Vulcans and the Andorians make a claim to a small planet and military conflict soon erupts. As the fighting goes on, the Vulcans announce they are willing to discuss cease fire terms.
The Enterprise crew find a small craft drifting in space and are surprised to find it contains a human corpse. More questions arise when both the Suliban and Tholians make claims to the craft.
Archer and Tucker are wrongly arrested and placed on a prisoner transport heading for a penal colony named Canamar.
Non-corporeal aliens possess the bodies of the Enterprise crew.
Archer is put on trial for crimes against the Klingon Empire.
Travis's visit home to the ECS Horizon becomes rather turbulent, as he clashes with his brother, the ship's new captain, and as the ship is attacked by pirates.
When militants take over a world, the Enterprise crew move to evacuate Denobulan geologists that are deep underground.
The Enterprise crew makes first contact with the Vissians, a species with three genders. When Trip meets one of the species' third gender, known as Cogenitor, he is disturbed to learn that all cogenitors are treated extremely poorly.
The remnants of an alien ship and two frozen cybernetic bodies are uncovered in the Arctic by a research team. These aliens soon thaw out and flee Earth, taking the research team with them.
Archer tells T'Pol the story of when he and a rival named A.G. Robinson were in competition for breaking the warp 2 barrier.
Archer learns the Klingons have put a price on his head when he is captured by a Tellarite bounty hunter. As Enterprise pursues, a virus causes T'Pol to go into premature Pon Farr.
An alien race known as the Xindi launch an attack on Earth, causing great casualties and massive damage.