On the bridge of the USS Defiant – having just witnessed the destruction of the ISS Enterprise by the Tholians – Commander Archer supervises Chief Engineer Tucker, T’Pol, and Major Reed, as the team desperately try to escape from a Tholian drydock that holds the Defiant. Even though they manage to shake the starship free from the facility’s docking clamps with the ship’s deflector shields, six Tholian ship approach and speedily construct an energy net over the opening of the dock, effectively barring the Defiant‘s escape.
With T’Pol’s assistance, Tucker manages to restore power to the Defiant‘s weapon systems from the bridge’s engineering station. The ship then blasts its way out of the dock, destroying half of the Tholian ships in the process and continues maneuvering away, firing aft photon torpedoes at the Tholian facility while departing. Reed detects escape pods from Enterprise, so Archer orders that they be brought aboard.
As the Defiant continues on impulse power, Archer confers with his officers, including Doctor Phlox and Hoshi Sato, in the ship’s briefing room. He demands that Tucker carry out the difficult task of restoring the advanced ship’s warp drive, and T’Pol suggests using the expertise of the alien slave workers aboard to do so. Archer implies an agreement with T’Pol’s recommendation. Although he plans that the ship will rendezvous with the Terran Empire‘s assault fleet, T’Pol argues that they are unprepared for battle. Archer insists on his plan and dismisses the other officers, but ensures T’Pol stays behind. He is furious that she betrayed him while aboard Enterprise. Now that Captain Forrest is dead and T’Pol finds herself threatened by Archer, she pledges allegiance to her new commanding officer, who claims the only reason she is still alive is that he needs her to help run the Defiant. Finally, after threatening her with death if he hears so much as a rumor that she’s working behind his back, he angrily dismisses her.
Hoshi Sato later arrives at the captain’s quarters and is amused to find Archer proudly adorned in a tunic belonging to the Defiant‘s former captain. After discussing the uniform, Archer tells Sato about the parallel universe that the Defiant is from, having reviewed the ship’s databanks. While she pours him a green drink, he says that the other universe has no Terran Empire but that Earth instead is a founding member of the United Federation of Planets. Archer and Sato humiliate one another by showing each other the service record of the other’s counterpart, Sato finding that Archer’s duplicate was a highly successful Starfleet officer. Archer finds difficulty with accepting that his own counterpart was so instrumental in the Federation’s founding. Sato tries to distract Archer with thoughts of his own promising future but, when she mentions that Starfleet will have to give him a command of his own, Archer declares he already has that – the Defiant.
At a vertical Jefferies tube, Tucker is irritated by Ensign Kelby reporting that a pair of plasma regulators have recently gone missing from the tube’s interior. Tucker threatens Kelby to find the regulators, or be made responsible for the Defiant‘s inability to go to warp. After Tucker hurries away, Kelby climbs into an access tunnel above, hearing strange rattling. He finds one of the regulators lying on the floor but is pulled headfirst into a Jefferies tube directly above him.
On the bridge, Phlox reports to Archer that evidence regarding Kelby’s death indicates the killer was a large reptilian. T’Pol, Reed, and Phlox discuss the reptilian. Tucker arrives and irritably comments that, without the plasma regulators, the ship is stuck at impulse, indicating – as T’Pol deduces – that the saboteur was well-acquainted with the ship’s systems. Reed enthusiastically approves with Archer ordering him to bring one of the alien slaves to the briefing room.
In the briefing room, Archer brutally interrogates a blue-skinned alien, who fears the reptilian will kill him and is therefore initially tight-lipped. Archer pressures the slave by pushing a phaser into his neck, threatening to disintegrate him with the weapon. This eventually makes the alien divulge information about the reptilian saboteur – a slave-master named Slar who was responsible for gutting the ship and whose species is Gorn.
On the bridge, Reed shows Archer a schematic of the Defiant on the viewscreen and updates him on the search for Slar, who recently escaped from Reed’s MACOs. Archer sees a hallucination of his counterpart from the Federation universe, who criticizes the lengthy search effort and boasts about how he handled a similar situation. A frustrated Archer directs Reed to form an assault team that Archer himself will lead. From the communications station, Sato detects Slar but cannot pinpoint his location. Archer contacts the Gorn but is unwilling to negotiate the return of the plasma regulators in exchange for allowing Slar to leave in a shuttlecraft. Eventually, Slar abruptly ends the transmission. Archer reminds Reed to form the assault team and explains to T’Pol, as he heads off the bridge, that he is skeptical of the Gorn’s sincerity.
Inside a turbolift, Archer’s hallucinatory double reappears, whispering to him that defeating Slar will finally earn Archer the respect he deserves.
Archer later leads the assault team – including Reed and four MACOs – through the ship, first heading up a vertical Jefferies tube and into an access tunnel. Reed and two of the MACOs fall victim to a trap, however, and are downed by a remotely triggered explosion.
He and the remaining MACO near the Gorn’s location silently search a corridor that is strewn both with exposed internals of the ship and with the bodies of several deceased officers.
Archer passes directly beneath Slar, without noticing it. He gives the MACO an all-clear signal, moments before Slar plummets down on Archer, causing him to drop his phaser. As he and the MACO assault the Gorn, it scratches Archer’s torso before turning its ferocious attention on the MACO, who Slar picks up and slams into a bulkhead. The Gorn approaches Archer as he quickly contacts T’Pol, instructing her to increase a certain section of the gravity plating. Her doing so drags the Gorn to the deck. Joined by two MACOs from a nearby turbolift, Archer repeatedly shoots the Gorn 6 times, killing Slar.
As the Defiant proceeds at warp, T’Pol and Phlox sit together in the officers’ lounge.
Phlox reveals to a curious T’Pol that Reed could just as likely die as survive and that he himself has been researching classical literature of both universes. With the exception of the consistently grim playwright Shakespeare, Phlox has a lowly opinion of the other universe’s stories, finding the characters to be weak and compassionate. T’Pol begins to speak of the Federation’s equality but Phlox fears the danger that the crew could learn such discoveries. Their conversation is interrupted by a call to battle stations.
Meanwhile, the NX-class starship ISS Avenger rushes out of a debris field, under attack by four rebel vessels in pursuit. The Avenger is fighting a losing battle, with Admiral Black assuming command from a dead captain. However, the Defiant soon arrives and speedily dispatches three of the rebel ships, despite T’Pol trying to dissuade Archer from destroying a Vulcan cruiser. He leaves an Andorian ship to warn the other rebels of the mass destruction and then contacts Admiral Black, who is puzzled by the absence of Enterprise. Archer says the situation will take time to explain and invites the admiral aboard the Defiant.
Returning from a tour of the ship, Archer and an impressed Black later enter the briefing room, accompanied by Sergeant Mayweather, the Avenger‘s Vulcan second-in-command (Soval) and a guard of the admiral’s. As the admiral refuses to grant Archer a battlefield commission to captain of the Defiant and Archer is teased by an illusory reappearance of his own duplicate, he insists that he is already a captain and – immediately after Mayweather kicks the admiral’s guard to the deck – Archer disintegrates Black with a phaser.
With Avenger and the Defiant traveling side-by-side, officers from both ships are gathered in Avenger‘s launch bay and watch Archer make a dramatic spiel, gradually moving from a walkway above the bay to a kneeling position atop a shuttlepod. He lengthily criticizes Starfleet Command for having allowed the recent annihilation of the assault fleet and rallies the officers to his cause against Starfleet Command, proposing that they utilize the Defiant‘s advanced capabilities.
Later, T’Pol and Soval have a conspiratorial meeting in the latter Vulcan’s quarters. Soval remarks that T’Pol’s use of a Vulcan salute, upon her arrival, is socially hazardous. She confirms that he read about the Federation, from the Defiant‘s historical database. Fearing that Archer will decimate the Vulcan species and their homeworld, T’Pol appeals for Soval to help her betray Archer, suggesting that she acquire the Defiant‘s schematics before giving them to the rebels. Soval at first argues against her and is alarmed by her announcing that she will destroy the Defiant but he eventually acquiesces to her intentions.
Meanwhile, Archer and then Sato – the captain’s woman – sit up from the bed of the captain’s quarters, which are now darkened. Archer worries that his senior officers, particularly T’Pol, doubt that he can succeed. Attempting to reassure him, Sato suggests disposing of T’Pol, now that the Defiant is operational. Archer suddenly reveals he is intending to transfer all the non-Terrans off the ship but Sato reminds him that Phlox is one of those aliens. As the couple begin to passionately caress each other, Archer accepts that Phlox can remain aboard, as his species are not rebels, and Sato wonders what will be required in the role of the Emperor‘s consort, to which Archer says she seems to have mastered the basics.
On the bridge, T’Pol secretly downloads Defiant‘s schematics from the science station. After arriving on the bridge with Mayweather and a MACO, however, Archer not only orders that he be put in contact with Fleet Admiral Gardner, but also directs the MACO to escort T’Pol to transporter room two. Just before she leaves, Archer makes it clear to T’Pol that she is no longer needed nor wanted aboard the ship. Gardner appears on the viewscreen and is furiously astounded that Archer has had the gall to demand Starfleet’s “unconditional surrender.” Explaining that Admiral Black is currently unavailable, Archer exchanges threats with Gardner over the consequences of whether the Defiant is permitted access to Earth, though the Fleet Admiral is far more serious in his demeanor. He warns Archer that the Defiant will be fired upon if it continues to approach Earth, then cuts the channel.
While walking through a corridor of the Defiant, Phlox is signaled by an intercom with a request for his immediate presence aboard the Avenger, apparently due to an unspecified medical emergency. Soon after arriving there, however, he finds that neither T’Pol nor Soval are injured.
On the walkway above Avenger‘s launch bay, the Vulcans attempt to convince Phlox to join their mutinous crusade. The doctor is initially astonished that they want him to sabotage the Defiant. Although he continues to dispute their ideas, Phlox starts to become convinced to join them, after the Vulcans tempt him by imagining what the Emperor might grant him in return for saving his life from Archer, such as an unlimited number of concubines. Ultimately, Phlox justifies the Vulcans’ plan to himself.
T’Pol later hurries through a corridor aboard Avenger but is confronted by Hoshi Sato and a MACO, who have phase weapons poised at the ready. Sato demands to know where the downloaded schematics are, but T’Pol feigns mere confusion. Despite Sato trying to take T’Pol back into custody, the Vulcan repeatedly attacks the MACO and a fight ensues between T’Pol and Sato, the women exchanging catty insults. T’Pol eventually knocks Sato to the deck, but her attempted escape is thwarted by the MACO, who stuns T’Pol with his own particle rifle. Standing back up, Sato orders the MACO to bring T’Pol with them.
Meanwhile, Phlox sneaks into a Jefferies tube aboard the Defiant and Soval oversees the securing of the Avenger‘s bridge, an Andorian male and an Orion female manning the helm and tactical stations, respectively.
Having learned of T’Pol’s most recent mutiny against him, Archer talks with her in the briefing room, having obtained her copy of downloaded Defiant schematics, while Sato sits nearby. An uncooperative T’Pol contends that an alliance like the Federation is inevitable in their own universe and that Humanity will eventually pay for its arrogance.
Phlox begins to sabotage the Defiant from inside an access tunnel and is, at first, assisted with vocal commands from Soval, who remains on Avenger‘s bridge. Aboard the Defiant, the sabotage results in a power drain developing, which Tucker decides to personally investigate. Aided by the gradual loss of the Defiant‘s total power, Avenger launches an incessant offensive against the Defiant, aboard which Tucker finds and battles Phlox. After managing to floor the saboteur, Tucker re-energizes the Defiant, restoring the craft’s shields and weapon systems. The Defiant retaliates against Avenger, which Archer purposefully destroys.
Later lying down on their bunk while drenched in sweat, Archer tells Sato to delete the historical database on the following morning. As Sato hands him a glass from the floor and takes one for herself, Archer fears that anyone else might become inspired by the Federation. The couple toast their drinks to his plan before Sato changes the subject of discussion, wondering if he thinks Starfleet’s commanders will support him. Archer believes they are consistently loyal to whomever holds the title of Emperor and, upon considering the start of his own reign, he pours a celebratory drink into his throat while holding his glass in the air. He continues to plot his reign but his words become thready and he collapses to the floor, clutching his chest in agony. After rushing to the room’s door, Sato opens it for Mayweather, who she passionately kisses while a pained Archer watches, realizing she has betrayed him before he loses consciousness.
The Defiant orbits Earth as Sato enters the bridge, accompanied by Mayweather and a MACO. At her instruction, Fleet Admiral Gardner appears on the viewscreen. Sato threatens the admiral that the Defiant will attack Earth if Starfleet does not immediately surrender. She identifies herself, to a perplexed Gardner, as “Empress Sato” and advises him to await her commands.