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Season Two
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Season Two Episodes
 Shockwave, Part Two
Intent on stopping Archer and Enterprise's mission, the diabolical Suliban take the crew hostage when it is discovered that Archer has mysteriously disappeared off the ship. While stuck in the decimated remains of the 31st century, Archer and Daniels work to find a way to get back to Enterprise; and Daniels worries that the future existence of The Federation may be in jeopardy as a result of his impulsive action to remove Archer from Enterprise, forever changing the course of history.
 Carbon Creek
T'Pol tells Archer and Trip a story about her great-grandmother T'Mir and three other Vulcans who made first contact with humans after crash landing in a small Pennsylvania town in the 1950s. T'Pol's story shocks Archer and Trip because her account is much earlier and very different from what history books reported.
After unwittingly wandering into a minefield in Romulan territory, Enterprise becomes trapped when struck by an undetonated mine. When Reed takes a space walk to try to defuse the mine, he inadvertently gets pinned to the outer hull and Archer must choose between saving Reed or abiding by the Romulans' orders to depart immediately.
 Dead Stop
Enterprise, in desperate need of extensive repairs, docks with a mysterious, high-tech, automated space station that inexplicably and amazingly fixes everything, making it almost too good to be true. While waiting for the repairs to be completed, the Enterprise crew searches the unmanned space station and discovers its unique and horrifying power source.
 A Night In Sickbay
Archer spends a fretful night in sickbay with Dr. Phlox after Porthos, Archer's pet beagle, picks up a deadly virus on an alien planet. Meanwhile, crew members believe Archer's increased stress level is due to Porthos' illness, but Dr. Phlox suspects it has to do with Archer's repressed sexual tension and urges Archer to discuss it with T'Pol.
When Enterprise is in need of fuel, Archer discovers a desolate mining colony that is being controlled by Klingon marauders who are bullying the colonists and hoarding their fuel. After Archer discovers the problem, the crew trains the colonists to defend themselves and prepare for a final showdown against their Klingon oppressors.
 The Seventh
T'Pol brings Archer with her on a top-secret mission when she is dispatched by the Vulcan High Command to capture a fugitive that has eluded their authorities for nearly two decades. Meanwhile, T'Pol reveals to Archer a dark and violent secret that she repressed, and Trip, who fills in for Archer while he is away, finds the weight of being the Captain hard to bear.
 The Communicator
Reed accidentally leaves his communicator on a pre-warp alien planet during a visit, and when he returns with Archer to retrieve the crucial technology, they are captured by soldiers who accuse them of being enemy spies. Meanwhile, Trip and Mayweather use the cloaking technology of the damaged Suliban Cell-Ship they had previously captured in an attempt to rescue Archer and Reed before they are executed.
On a "typical" day on Enterprise, the crew finds their routine tasks turn into uncharacteristically strange obsessions over trivial matters.
 Vanishing Point
Following her first experience in the transporter, a series of eerie events leads Hoshi to question whether she is the same person.
 Precious Cargo
Trip rescues an exotic alien woman from her kidnappers, but ends up on an unexpected romantic adventure.
 The Catwalk
When a deadly radioactive storm threatens Enterprise, the entire crew must take refuge for eight days in a small maintenance shaft.
Trip is fired upon by a territorial alien and forced to land on the night side of a moon.

T'Pol's standing on Enterprise is threatened when it is learned that she has contracted a deadly disease.
 Cease Fire
When a military conflict erupts between the Vulcans and Andorians, Archer is brought in as negotiator.
 Future Tense
Enterprise finds a small craft adrift in space that contains what appears to be a human corpse, one the Suliban and the Tholians both try to retrieve.
Archer and Tucker are mistakenly arrested and placed on a prisoner transport vessel bound for the penal colony Canamar.
 The Crossing
Enterprise is swallowed by an otherworldly vessel occupied by noncorporeal creatures who seek to trade consciousnesses with the crew members.
Archer stands accused before a Klingon tribunal of conspiring against the Empire, and faces a lifetime sentence on Rura Penthe.
While Enterprise investigates a planetary phenomenon, Mayweather takes the opportunity to visit the cargo ship where he was born and raised.
 The Breach
Enterprise is asked to evacuate a group of Denobulan geologists from a world that has been taken over by a militant faction.
Enterprise encounters a race called the Vissians who feature a third sex of "cogenitors" who are treated as second-class citizens.
An arctic research team discovers debris from an alien vessel, buried in a glacier along with the bodies of two cybernetically enhanced humanoids.
 First Flight
While Enterprise is investigating a nebula, Archer hears that A.G. Robinson, his old rival in the early days of the NX test program, has died.
A Tellarite bounty hunter captures Archer intending to turn him over to the Klingons for a substantial reward.
 The Expanse
When a probe from an unknown alien source unleashes a devastating assault upon Earth, Enterprise is recalled, then sent to search for the perpetrators.