Set in 2151, over a century before Kirk's voyages in Star Trek lore, and only 150 years ahead of our own time, Enterprise set out to explore a whole new world of the unknown. Earth's people have only just perfected the Warp 5 engine and a whole deeper region of space beckons. But in spite of the Vulcans' misgivings, whose "aid" many see as condescending and cautious, the humans strive to realize their potential.
Jonathan Archer quickly assembles a crew and launches ahead of schedule to return a wounded Klingon to his people using Earth's first Warp 5 starship, the Enterprise NX-01. But humanity's first truly deep-space mission turns sour when Archer is forced to take aboard a Vulcan first officer and the Klingon is later abducted by mysterious aliens. (First of two parts)
Against the advice of his dour Vulcan liaisons, Archer and his crew set out to recover the kidnapped Klingon themselves, and become ensnarled in the Temporal Cold War and the genetically altered Suliban under Silik who fight for one faction involved.
Discovering a derelict ship, Archer's crew finds the incapacitated aliens aboard being drained of a vital body fluid. The attackers return and fire on Enterprise, but the victims' rescuing brethren mistake the humans for enemies as well unless Hoshi can perform a translation miracle and even the odds in the standoff.
Landing on an unspoiled world, Archer allows an away team to make the ship's first on-site planetary survey and then spend the night there. Storms force the team into a cave for shelter, where a pollen unwittingly causes a deep and nearly fatal paranoia among Tucker and T'Pol that Archer is nearly powerless to overcome.
When a cloaked and damaged Xyrillian ship is discovered draining warp plasma from the Enterprise, Tucker is sent to help and winds up flirting with one of the alien women, getting a look at a complex holographic environment. But reality returns later when he finds the non-sexual encounter left him pregnant!
Now distant enough from Earth to probe the fate of a lost troubled colony from 75 years earlier, the Enterprise orbits Terra Nova but finds only a colony of cave dwellers, who ambush the landing party. Unusual radiation readings provide one clue, but then the captives discover an even bigger surprise.
An innocent visit to the Vulcan monastery on P'Jem leaves the NX-01 crew in the middle of a fight between their hosts and the blue-skinned Andorians, who insist the site is a front for a high-tech listening base. Archer's honesty and honor forges a new and long-running bond with Shran, the Andorian commander, as the antennaed species makes its first major appearance since the original Star Trek series.
Reed and Mayweather are sent to mine a rare mineral from a large comet, while the Enterprise maintains frosty contact with a Vulcan captain maintaining his planet's patronizing attitude toward humans. Then the comet crew are endangered, and Archer must swallow his pride to ask for help.
Encountering a new civilization on Akaali, Archer discovers that another space-faring culture has already made contact. But when an Akaali women blames the visiting Malurians for a widespread sickness, Archer and his staff don Akaali disguises to probe the Malurians covertly.
Responding to a distress signal from an Earth freighter which has been attacked by Nausicaan pirates, Archer finds the freighter's crew is torturing a Nausicaan prisoner for information. With his superior incapacitated, the freighter's young acting captain is unrepentant despite the Starfleet crew's demands.
Among a religious group visiting the Enterprise, one pilgrim turns out to be the disguised Suliban leader Silik -- but his act of "sabotage" actually saves the starship from later destruction in a plasma storm. The onetime adversary's puzzling aid brings on another revelation: the first recurring appearance of Daniels, a temporal agent from the 31st century who, though posing as one of Archer's crewmen, needs his help while tracking Silik and other Temporal Cold War factions.
While the Enterprise fends off attacks from an alien vessel that refuses to communicate, Hoshi tries to discover Malcolm Reed's favorite food in time for his birthday. She comes away learning more about the lieutenant than the crew ever finds out about its mystery encounter.
When the Valakians ask for help with a planet-wide plague, Phlox realizes that the problem is genetic: the species is doomed in 200 years unless the immunity of the Menk, a simbiotic people that peacefully share the planet, yields a clue. But Phlox's cure brings up the ethics of interfering in natural selection: the Valakians' extinction would allow the Menk to fulfill signs of further blossoming. A soul-searching Archer agrees with him: the Valakian species is prolonged but not cured, in order to avoid "taking sides."
Detecting a disabled Klingon ship in the atmosphere of a gas giant, Archer sends an away team to assist and revive its crew as a goodwill gesture. But finding human help dishonorable, the Klingons' lack of cooperation instead leaves the team trapped on the doomed ship.
Blaming Archer for the Andorians' destruction of their P'Jem monastery after it was unmasked as a front for spying, the Vulcans insist on recalling T'Pol for reassignment. But the two planets' dispute embroils Archer and T'Pol on an away mission on Coridan, where they are rescued by unlikely allies and expose the factions at play.
After conducting targeting tests well away from the Enterprise, Tucker and Reed believe themselves marooned when they return but find evidence the NX-01 has been destroyed. Even worse, they lose containment and have no way to reach safety before running out of air -- so death's approach provides a bonding experience like no other.
The Enterprise encounters a vessel manned by Vulcans who explore their emotions and use the mind-meld, practices frowned upon by mainstream Vulcan society. Although reluctant to associate with them, T'Pol finds herself intrigued by their experiences, and she becomes changed forever.
On a dark planet which has broken free from stellar orbit, Archer's away team encounters an Eskan hunting party tracking a wraith. Approached by a beautiful woman apart from them, the captain learns that the "wraith" is a native shape-shifter who desperately needs his help.
The Enterprise crew is knocked out and robbed by four pirates from a short, big-lobed species they have never met before. Once awake, Archer realizes that the way to regain control is to play to the pirates' greed, but he never does learn of their background -- so real first contact with the Ferengi has to wait another hundred years!
Intrigued by stories of a "haunted ship" that crashed years before, the Enterprise crew finds the site and soon sees figures who do not register on sensors. When a desiccated corpse is discovered, the strange tale that unfolds is not what they expected.
Having trespassed in the Tandaran military zone, Archer and Mayweather are held in a prison amid civilian Suliban who are routinely held even though they are not the genetically altered troops led by Silik in the Temporal Cold War. Disgusted that the innocent detainees include children, Archer organizes a jail break.
After a disastrous diplomatic meeting, the Enterprise is invaded by a strange web-like creature that takes up a corner of a cargo bay, ensnaring Archer and several of the crew. Aided by Reed's pioneering use of a force field, Hoshi must find a way to communicate with it or else risk a rescue that could kill their fellow officers.
Archer receives orders to transport the Vulcan Ambassador V'Lar from the planet Mazar, where she is being deported over criminal charges. T'Pol cannot believe such disloyalty is possible from her onetime role model, found to be an unusually open Vulcan, but the elder's mum response to the charges only leaves T'Pol cold and Archer curious.
Having repaired a crippled ship, Archer and Tucker are invited by its captain to dinner on his desert planet. When the host's camp is attacked, the two officers learn he is a terrorist seeking their aid for his side -- if they survive their flight into the desert to escape.
Finally arriving at resort world Risa for a long-due break, the crew draws lots for taking shore leave. Hoshi, Tucker, Reed, Archer and even Porthos find companions for the short stay, but each sees their leave time turn out in totally unexpected directions -- while Phlox gets in some Denobulan hibernation time aboard ship.
When Reed's shuttlepod apparently causes an atmospheric explosion that kills an entire Paraagan colony, the Enterprise is recalled to Earth to end its mission in disgrace. Temporal agent Daniels visits Archer to help him retrieve the truth, but during a Suliban encounter the two men wind up in a wrecked future Earth of an altered universe, shockingly cut off from time travel and any means to repair the damage. (First of two parts)