April 5, 2063 – From beyond Earth‘s atmosphere, a Vulcan ship descends and lands in Bozeman, Montana. Watched by a crowd of onlookers, a member of the Vulcan crew disembarks and approaches Zefram Cochrane. The alien performs a Vulcan salute and recites a Vulcan salutation: “Live long and prosper.” Cochrane tries to imitate the newcomer’s salute. After an unsuccessful attempt, he lowers his hand and, instead of holding it for a handshake, he reaches into his coat and pulls out a shotgun with which he shoots the Vulcan, who instantly collapses. A bearded man in the crowd tells the other Human spectators to board the alien ship and take everything they can.
Aboard the ISS Enterprise, Reed and Phlox demonstrate their new invention, an agony booth, to Captain Forrest and First Officer Jonathan Archer. The observers discuss attributes of certain torture methods, after what Captain Forrest exits, followed out by Archer.
In a corridor, Archer reminds the captain of a proposal he made to venture into Tholian space, to retreive a technology that would give the Terran Empire the upper hand against a rebellion. However, Forrest wants to help the Empire’s assault fleet annihilate the rebels, as ordered by Starfleet. Although Forrest suspects that Archer wants to use the technology to attain personal glory, the first officer repudiates this. Archer’s insistence on his plan influences Forrest to threaten the first officer with a place in the agony booth. Archer finally yields to Forrest’s authority.
Forrest is later busily reviewing work in his quarters when Hoshi, the captain’s woman, approaches, eager to relax him. Hoshi remarks that she is likely the only person aboard who doesn’t want to kill him. Relaying rumour that a recent battle with the rebellion at Tau Ceti went well, Hoshi plans that – once the war is over – she will return to teaching students in Brazil while Forrest will accept a desk job at Starfleet Headquarters. He, however, explains that the battle was much worse than she has heard; Forrest implies that he is hiding the truth from the rest of the crew. Hoshi advises him to forget about the war and goes back to passionately kissing him.
As Enterprise warps through space, Forrest is making his way through the ship, closely followed by a MACO, when they are ambushed by Archer and some MACOs allied with him, including Reed and Mayweather. Despite Archer ordering Reed to lock Forrest in the brig, the Major is intent on killing the imprisoned captain. Archer threateningly insists that Forrest be kept alive, so Reed ultimately relents.
T’Pol is sitting in the bridge‘s command chair when Archer and his MACOs arrive. Archer seizes control of the bridge and – via a ship-wide communication that is heard by Hoshi, Phlox and the disfigured Chief Engineer Charles Tucker – he assumes command of the rest of the ship, claiming that Starfleet ordered not only his takeover, but also that he direct the ship on a vital, secretive mission into Tholian space. He assures the crew that if their mission is successful, Starfleet will crush the rebellion once and for all. He oversees the ship’s change of course and orders T’Pol to help with the installation of a stored Suliban cloaking device, as it will be necessary to the mission.
In the captain’s ready room, T’Pol reluctantly accepts that Archer is in command. He shows her Zefram Cochrane’s shotgun from a century prior, wondering what might have happened if Cochrane had not used it to kill the first Vulcan who set foot on Earth. T’Pol then lets Archer know that they have likely entered Tholian-occupied space. Archer assigns her to search for a particular warp signature and, just as she is about to leave, he calls her back in with news that he is promoting her to first officer, Finally dismissed by Archer, T’Pol exits.
Later, Archer personally promotes Sergeant Mayweather to acting as the Captain’s personal guard. Mayweather starts to congratulate Archer on his successful mutiny but the newly appointed captain cuts him short, followed by snarls from a hungry Porthos. Hoshi arrives, and admits that she knows Archer didn’t receive orders from Starfleet. He shows her an image of the brig on his desktop monitor and says the former captain will stay alive as long as Hoshi cooperates. Although she seduces Archer into accepting her continuance as the Captain’s woman, she pulls a knife out while they kiss. He disarms her, just as T’Pol hails him. The Vulcan reports that Enterprise is approaching the sought-after warp signature.
Enterprise drops out of warp, nearing its target: a Tholian ship, manned by a single Tholian. Following a failed plan to tractor onto the enemy craft and a subsequent brief exchange of firepower, Enterprise disables the Tholian ship. Its pilot starts an overload in its reactor but is beamed into Enterprise‘s Decon chamber just as its own ship explodes. Acting on orders from Archer, Phlox delightedly begins to torture the Tholian by modifying the chamber’s atmosphere.
The senior staff gather outside the Decon chamber. Archer is interested to know where the Tholians have taken a Terran vessel they captured. Phlox tortures the prisoner until it admits that Archer’s quarry is at an orbital facility in the Vintaak system. The Tholian then starts using its own crystalline structure to transmit a distress signal. Archer lets his senior officers know that he would prefer to keep the alien alive but unconscious until its information is confirmed.
Working with T’Pol on installing the cloak in Engineering, Tucker sees to it that she has a radiation meter from engineering officer Biggs, as it will prevent her from absorbing the same kind of delta rays that disfigured him. Discussion turns, much to T’Pol’s discomfort, to a past experience wherein Tucker allowed her to relieve pon farr with him. An electrical overload sparking to the cloaking device electrocutes Tucker.
Archer and Reed later inquire into the incident. The captain is insistent that Tucker prioritize the cloak’s repair. Reed is suspicious of the overload, but Tucker objects to Reed’s MACOs investigating.
In the brig, Archer demands that Forrest identify the saboteur, believing it was a spy assigned by Admiral Black, but Forrest claims ignorance. Archer orders Mayweather to search the captain’s quarters for telltale messages from Starfleet. Now alone with Archer, Forrest criticizes him of having always lacked ambition. Archer brutalizes Forrest, citing his imprisonment as a sign that he is incorrect. Forrest pleads for Archer to release him, claiming consequences of both freeing him and killing him. Archer throws him against a bulkhead and departs.
In the bridge’s situation room, Reed explains to Archer that evidence points to Tucker as being the saboteur. Tucker is later punished in the agony booth. Through severe pain, Tucker claims he is innocent and threatens Reed for having implicated him, but Reed merely teases Tucker in return. Archer suspects Tucker is Admiral Black’s spy and, despite Tucker insisting to the contrary, a distrusting Archer directs Reed to continue subjecting Tucker to the agony booth.
Later in the captain’s quarters, Archer and Hoshi lie together, clearly having had sexual intercourse. The captain ensures that Hoshi transmitted data to the fleet admiral but only refers to it cryptically, as an “insurance policy.” Archer then starts to suspect T’Pol of being the saboteur, finding that she cannot be located by the ship’s computer as the overload damaged the internal sensors.
T’Pol meanwhile leads a successful rescue effort to free Forrest from the brig, two Vulcan companions of hers having a brief encounter with Archer, who escapes in a turbolift. Forrest and T’Pol then retake command from the bridge but find that the ship is locked on course, which Archer personally confirms before sarcastically relinquishing command to Forrest.
With Archer having spent ten hours in the agony booth, Phlox remarks to Captain Forrest that he is amazed by Archer’s pain threshold. The captain is reluctantly forced to release Archer from the booth. Forrest not only wishes to instead use it on Major Reed, but also privately informs Archer that Fleet Admiral Gardner has ordered his release, having been intrigued by the data Archer sent via Hoshi. A seething Forrest lets Archer know that his betrayal is unforgivable and notifies Archer that he is due to brief the senior staff in an hour.
While Enterprise continues at warp speed, the senior staff are gathered in the briefing room. Archer is briefing the senior staff, explaining that – after managing to open an interphasic rift into a parallel universe – the Tholians intentionally lured a ship through from the other side. Archer shows the other officers some images of the captured ship. The assembled crew members muse over the significance of the craft, which Archer says is not only from another universe but also from about a hundred years into the future. T’Pol strongly objects to the information, fearing it is a trap and reminding Forrest of Archer’s crimes, but Forrest insultingly interrupts her – adamant that they will investigate the ship – and instructs Tucker to get the cloak working.
While working on the cloak in Engineering, Tucker becomes distracted by T’Pol’s presence and vents his anger at her for having apparently falsified the evidence that incriminated him earlier. She explains that she seduced him away from engineering before motivating him, by way of a mind meld, to sabotage the cloak himself, before using another meld to alter his memory of what had happened. She states that she was duty-bound to help Forrest regain command. Tucker calls the bridge and reports that the cloak is ready, so Forrest orders for it to be engaged. The ship encounters slight energy fluctuations at first, but then cloaks.
Soon thereafter, T’Pol is at the bridge’s science station when Enterprise reaches its destination, in proximity of a gas giant in the Vintaak system. The bridge officers spot the captured ship in a drydock built into a moon of the gas giant. The vessel is the Constitution-class Federation starship USS Defiant.
T’Pol briefs Archer, Tucker, Reed and Forrest in the situation room, telling them that Defiant‘s systems, even that of life support, are powered down. Those alive aboard the Defiant consist of thirteen non-Humans, including one reptilian. Although Tucker is impressed by the vessel’s engineering capabilities, Forrest plans for Archer to lead an assault team to salvage as much as possible from the craft’s databanks before destroying it. Archer objects to this plan but Forrest shouts him down. Moments after the others leave, Forrest instructs T’Pol to join the assault team, conspiratorially implying that he wants her to ensure Archer dies during the mission.
Wearing environmental suits, the team (now including Sergeant Mayweather) beam into a corridor of the Defiant to find that the Tholians have been gutting the vessel. The team also come across a dead Human security officer lying beside a discarded phaser. Reed offers to hold the weapon but Archer takes it instead.
On Enterprise, a sedative that Phlox has been using on the Tholian pilot stops working and the alien begins retransmitting its bodily distress signal. After the signal is detected on the bridge, Forrest contacts Phlox, ordering him to kill the Tholian. Doing so takes time and Phlox becomes impatiently frustrated. He eventually succeeds in destroying the Tholian but its communication has attracted the attention of three Tholian vessels that approach Enterprise and start to hail the ship.
The assault team meanwhile arrive on the Defiant‘s darkened bridge. They find only two deceased officers there, one of whom is a man wearing a command division uniform; Archer assumes he is the captain and T’Pol reports he has a broken neck. With Archer’s approval, Tucker begins attempting to repower the vessel.
Four more Tholian ships approach Enterprise and, despite an initial attempt by Forrest to withdraw from the mission, the alien vessels are not only jamming communications, but also subsequently create an energy web that surrounds Enterprise. Forrest first tries to fire the ship’s weaponry through the web, and then manoeuvrer out of it, but neither method succeeds; Enterprise is trapped.
Tucker’s eventual restoration of power to the Defiant‘s systems enables T’Pol to monitor Enterprise‘s situation.
Moments later, Forrest orders the crew to abandon ship but, much to Hoshi’s concern, he chooses to stay behind in the hope that he might be able to buy the survivors more time.
Archer orders that the Defiant‘s weapons and engine systems are brought back on-line and, with the help of Mayweather and Reed, he starts to remove the two dead officers from their positions in front of the command chair.
Enterprise meanwhile launches its complement of escape pods but many are instantly destroyed. Forrest holds on to the helm station of his dying ship, moments before the assault team watch through the Defiant‘s viewscreen as Enterprise explodes.