In San Francisco of the year 2121, a young Jonathan Archer paints a model of his father's spacecraft. When he recites a quote from a speech by Zefram Cochrane, Henry Archer tells him the inventor of the warp drive would be proud of him. Jonathan curiously asks about his father's ship, wondering if it will be bigger than "Ambassador Pointy's" ship. Henry corrects his son, noting that the Ambassador is actually named Soval, an extremely helpful Vulcan. Jonathan responds that – according to Billy Cook, an acquaintance of his – Humans would already be flying at warp five, if the Vulcans had not intervened. Although Henry Archer does not fully understand the reasons behind the Vulcans' constraint, he believes that there must be an explanation.
Thirty years later, the wreckage of a crashed Klingon K'toch-class scoutship lies in a cornfield in Broken Bow, Oklahoma, on Earth. Klaang, the Klingon pilot of the craft, desperately flees from two pursuing aliens. This incident attracts the attention of a farmer named Moore. Although Klaang eventually manages to kill the aliens, he is shot with Moore's plasma rifl.
Aboard Enterprise, Lieutenant Malcolm Reed and Ensign Travis Mayweather discuss the vessel's transporter, a brand-new piece of equipment first installed on their ship. As they walk through a corridor, Mayweather reminisces about his childhood aboard cargo ships. When they enter Engineering, Reed introduces Mayweather to Commander Tucker. Meanwhile, Archer travels to Brazil to recruit linguist Hoshi Sato as his communications officer.
Another addition to Archer's crew is Subcommander T'Pol, whose assignment for the position of executive officer and science officer was obligatory in exchange for the Vulcan star charts. In the captain's ready room, T'Pol is introduced to Commander Tucker by Archer and she gives him a PADD confirming her new assignment. An embarrassing encounter with the captain's dog, Porthos, then follows, since Vulcan females have an heightened sense of smell. Along with T'Pol – whom Archer saw as a Vulcan "chaperon" – the Doctor he met before, at Starfleet Medical, is also added to Enterprise's crew.
At Enterprise's launching ceremony, Admiral Forrest makes a speech and remarks there is no better person to captain the first Warp 5 starship than the son of its inventor, Jonathan Archer. After this, a recording of a speech by Doctor Zefram Cochrane is played, from the dedication ceremony of the Warp Five Complex, 32 years ago.
As these historic words are spoken, Archer remembers his childhood, when he and his dad placed an anti-gravity controller into the model. Mayweather then asks for instructions. He responds, "Take her out, Mr. Mayweather. Straight and steady." And so, the NX-01 Enterprise leaves spacedock and jumps into warp.
Astrange alien complex, an alien officer talks to a mysterious figure Meanwhile, in a strange chamber aboard an alien complex, a Suliban officer confers with a mysterious silhouetted figure and promises to recover evidence that the figure requires. This evidence apparently was in the hands of Klaang when he was pursued by the Suliban.
Aboard Enterprise, Archer observes a jar full of immunocytic gel worms in sickbay. The doctor he met earlier, a Denobulan in the Interspecies Medical Exchange program named Phlox, asks the captain to make sure that he doesn't shake the worms. Archer helps Phlox unpack medical equipment and an Altarian marsupial, an animal that makes the captain squirm because its droppings are used as medicine. Meanwhile, Travis Mayweather shows Commander Tucker the "sweet spot", an area of every ship where gravity is reversed. Mayweather is a well-traveled "space boomer" and has visited the planets Trillius Prime, Draylax, and both the Teneebian moons. Later, when Tucker enters the ship's mess hall, he is offered a seat by Crewman Fletcher but the engineer replies that he has already been asked to the captain's mess. There, the engineer eats with Archer and T'Pol while they discuss Human evolution.
However, all is not well – during a test of the ship's warp reactor, a verbal conflict between Hoshi Sato and T'Pol arises. When Ensign Sato insults T'Pol in the Vulcan language, the science officer retorts that she herself was instructed to speak English during her assignment aboard the ship and expects Hoshi to do the same. Later, the vessel loses main power while Archer, Hoshi and Phlox are in sickbay, trying to interrogate Klaang. Alien soldiers board Enterprise and attack the Starfleet officers. Klaang recognizes the aliens as Suliban and, although Archer manages to shoot one of the aliens, the Klingon is abducted from the ship.
On the bridge, an irritated Archer asks his crew why the Suliban were not detected by Enterprise's sensors. When Lieutenant Reed tells him that the starboard sensor logs did record a spatial disturbance, the captain orders the bridge crew to conduct a full investigation into the incident. T'Pol advises Archer to consult the astrometrics computer in San Francisco, believing that he himself has no hope of finding Klaang. However, the captain decides not to take her advice and forbids T'Pol from contacting Starfleet. In sickbay, Phlox shows Archer the corpse of the alien soldier that was left aboard Enterprise. The doctor has learned that the alien has Suliban DNA, but its anatomy has been altered by very sophisticated genetic modifications.
In engineering, T'Pol helps Tucker to review the sensor data. Archer and Sato soon enter. Using both Sato's translation of Klaang's words as well as T'Pol's reluctant assistance, Archer learns that Klaang visited Rigel X just before his scout ship crashed on Earth. The captain contacts the bridge and orders Mayweather to set course for the tenth planet in the Rigel system. Meanwhile, an alien officer aboard the Suliban complex interrogates Klaang in Klingonese. This Suliban officer asks Klaang where he left a particular unnamed item, but the Klingon claims ignorance. He tells the officer that he was sent to meet a Suliban woman named Sarin on Rigel X but that Sarin did not give him anything. As Enterprise approaches the planet, Archer and T'Pol brief an away team in the ship's launch bay. Archer informs the officers that Klaang was a courier and tells them to find the person who gave the Klingon whatever he was carrying, so they might find out why the Suliban have captured Klaang.
The team travel to Rigel X in Shuttlepod 1 and search in a trade complex on the planet's frozen surface. Reed and Mayweather are persuaded, by a man who claims that he saw Klaang, to watch a pair of alien females performing with butterflies. The pair of officers doubt the man's honesty and soon leave. While T'Pol investigates, Tucker finds difficulty with accepting several aliens that he encounters, including a Lorillian mother and son. Archer and Sato meanwhile catch a fleeting glimpse of a group of Klingons. Soon after, the entire away team is attacked and captured by Suliban.
Sarin offers to help Archer find the Klingon, but agents of the Suliban Cabal discover them and open fire. Sarin frees the Starfleet officers but is killed in the fight between the Cabal and her small group of renegade Suliban. Archer, injured while on the run, manages to escape in the shuttlepod. With a damaged thruster, the shuttlecraft ascends into the atmosphere as T'Pol contacts Enterprise and announces that she is taking command of the ship. When Captain Archer loses consciousness, he dreams about himself as a child flying his model spacecraft on a beach with his father. He is disappointed when the model crash-lands in the sand, and his father tells him that he can't be afraid of the wind as T'Pol watches from the shore.
After Shuttlepod 1 has returned to Enterprise, T'Pol and Tucker use the decon chamber to rid themselves of a protocystian spore they picked up on Rigel X. Here, Tucker questions whether he should take command rather than T'Pol, because she was only assigned to the ship as an "observer". The engineer worries that T'Pol will not continue the search for Klaang if she takes command.
Six hours later, Archer regains consciousness in sickbay. Phlox removes, from Archer's leg, an osmotic eel that the doctor used to cauterize the captain's wound. T'Pol and Tucker visit and the Vulcan informs Archer that they have tracked a Suliban ship that left Rigel X just after the captain was injured. Archer is surprised that T'Pol didn't order a course back to Earth, but the Vulcan states that, as acting captain, she was obligated to anticipate Archer's wishes. Archer responds that, as acting captain, she could have done whatever she wanted.
As Enterprise continues to follow the Suliban ship, Archer, back in his quarters, is making a log entry, pausing the log several times to question himself about T'Pol's motives to continue the mission.
Archer hears the warp drive changing and looks out his window to see that the ship has dropped out of warp. He contacts T'Pol, who asks him to come to the bridge.
There, a gas giant is displayed on the viewscreen. T'Pol tells Archer that the Suliban craft entered the planet's radiation belt a few hours ago, scattering the vessel's warp trail. T'Pol instructs Reed to run a spectral analysis on fragments he has detected nearby. The bridge crew finds that the fragments were left from fourteen different ships. Realizing that Enterprise has found an area used frequently by the Suliban, Archer orders Reed to activate the ship's weapon systems and to polarize the hull plating. The captain then directs Mayweather to set a course that will take the ship into the planet's atmosphere.
Aboard the alien complex, the Suliban officer talks with the mysterious figure. The officer is unsure whether Sarin gave the Enterprise crew anything, but he knows that Enterprise has followed a Suliban ship and is nearby. He promises the figure that he will destroy the Human vessel before it locates the Helix, the complex that he is currently on. The figure says that he didn't intend for Humans or Vulcans to become involved yet, and demands that the officer must stop Sarin's message from reaching Qo'noS.
In the atmosphere of the gas giant, Enterprise almost loses the warp trail. T'Pol estimates that the ship's condition should improve, shortly before the bridge starts to shudder. She uses a viewer at her station to determine that the quakes are being caused by unexpected liquid phosphorus. When the ship's condition improves, the officers detect two Suliban cell ships and the helix. Sato reads more than three thousand bio-signs aboard the alien station, but is unable to find Klaang with the ship's sensors. When Suliban ships start attacking, Enterprise returns to the phosphorus layer, where the enemy vessels can't find the Starfleet craft. T'Pol reports that the helix seems to be comprised of hundreds of other vessels, locked together by magnetic seals. When Sato finally detects Klaang aboard the complex, Reed suggests using the transporter to get him out but Archer finds Reed's plan too risky. The captain decides to use Enterprise's grappler to retrieve one of the attacking cell ships and bring it aboard Enterprise.
In the situation room, aft of the bridge, Mayweather questions Archer and Tucker about the workings of the captured Suliban vessel. As the engineer seems to be slightly unsure of the craft, Mayweather believes that he would make a better pilot. Archer replies that the ensign is needed on board Enterprise and Tucker believes that piloting the Suliban vessel won't be as hard as it seems.
In the captain's ready room, T'Pol attempts to discourage Archer from leaving. She suggests that he appeal for support from a nearby Vulcan ship. The captain suspects the Vulcan is displaying emotional concern, but T'Pol claims that the Vulcan High Command will hold her responsible if anything happens to Tucker or the captain. Reed enters, carrying two cases into the room – one holds a magnetic device and the other holds two newly designed weapons called phase pistols. According to the lieutenant, the weapons have two settings - stun and kill. He advises Archer not to confuse the two.
Archer and Tucker leave Enterprise and use the captured cell ship to travel to the helix, where they find Klaang. Although the Klingon is initially hostile, Archer threatens the alien with his phase pistol so he will cooperate with the captain's orders. Together, the three men move through the helix and attack any Suliban guard that approaches them. The captain instructs Tucker to return to the cell ship with Klaang while he stays behind and tries to separate the helix using the magnetic device. After doing so, Archer contacts Tucker and tells the engineer not to return for him, but to take Klaang to Enterprise. Tucker complies as several of the drifting enemy ships surrounding the commandeered cell ship collide.
Tucker ignites the cell ship's thruster exhaust, giving Sato, on board Enterprise, the opportunity to tell T'Pol what to look for. When T'Pol detects Tucker's position, she thanks Sato in the Vulcan language.
Aboard the helix, Archer fights with the alien officer. The alien nearly kills Archer with his own phase pistol, but the captain moves out of the way just in time. The alien chases Archer into another room where a strobing, pulsating light throbs. Just as the alien shoots again, Archer is beamed aboard Enterprise. Tucker apologizes for using the transporter, but claims it was the only way to recover the captain. Enterprise immediately leaves the gas giant at warp speed.
After arriving on Qo'noS, Archer, Klaang, Sato and T'Pol enter the Klingon High Council Chamber. As Klaang addresses the High Council in Klingonese, Sato tries her best to interpret his words. According to the linguist, Klaang says something about disgracing the Klingon Empire and mentions that he's ready to die. The Klingon Chancellor approaches Klaang and makes a small cut in his hand with a jagged dagger. The Klingons then pour some of Klaang's blood into a vial which they examine with a large scientific device. The extracted DNA from his blood contains a wealth of Suliban information. The Klingons shout in gruff approval, but soon quiet again. The Chancellor approaches Captain Archer and, holding the dagger against the captain's throat, says something in Klingonese that Archer interprets as a thanks. Once the Chancellor leaves, Sato comments that the captain's interpretation was incorrect, and claims that Archer wouldn't want to know what the Klingon actually said.
Aboard Enterprise, Archer tells his crew that the starship's mission is to continue. Tucker begins work on repairing the starship as Archer orders Mayweather to set a course for an inhabited planet nearby. Although there is an ion storm between the starship and its destination, the captain tells Mayweather that they can't be afraid of the wind.