In the Mirror Universe, an amoral, imperialistic version of the Enterprise crew is led by Captain Forrest and his treacherous first officer, Archer. Archer has proposed that the ship head into Tholian space, where a mysterious vessel has been captured. Archer believes the ship may contain the technology that would be valuable to the Terran Empire. Forrest, however, thinks Archer is merely trying to seize power, and dismisses the idea.
A determined Archer has another plan up his sleeve, however — with help from Major Reed and Sergeant Mayweather, he stages a mutiny, taking control of the ship and imprisoning Forrest in the brig. Archer promotes Commander T'Pol to first officer, appoints Mayweather his personal guard, and takes up with Forrest's lover, Hoshi.
As Enterprise approaches Tholian space, the crew captures a Tholian pilot. Phlox takes great pleasure in torturing the creature, who finally gives Archer the information he wants: the exact location of the mysterious vessel.
In Engineering, Trip and T'Pol work to install a Suliban cloaking device on Enterprise. Something goes wrong, however, and a power overload damages the cloak. Archer realizes it was sabotage, and Reed determines that the saboteur was Trip. Reed tortures Trip using the sadistic agony booth, but the engineer offers no further information. Later, Archer has another realization: the target of the sabotage wasn't the cloak — it was the ship's internal sensors. In fact, the actual culprit was T'Pol, who mind-melded with Trip and tricked him into performing the sabotage.
T'Pol frees Forrest from the brig and the duo takes control of the bridge. Archer, however, has a surprise for them: he's encrypted the ship's controls, and they won't be released until Enterprise has reached its destination in Tholian space. Forrest is furious, but there's not much he can do — especially when he is ordered to investigate the captured ship.
Archer briefs the senior staff on the ship: it is believed that the vessel came from a parallel universe via an interphasic rift. What's more, the ship isn't just from another reality — it's also from another time, about 100 years in the future.
Once Trip gets the cloaking device working, Enterprise heads for the coordinates of the future ship. The ship, which bears the name and registry U.S.S. Defiant, NCC-1764, is being kept inside a Tholian spacedock facility. Forrest sends an assault team, led by Archer, onboard. He tells T'Pol to accompany the team — and to make sure Archer doesn't come back alive. The team boards the ship, which is littered with dead human bodies. Still, they manage to bring the Defiant's systems online.
Onboard Enterprise, the Tholian prisoner wakes up and starts making a racket . Phlox kills it, but Enterprise's problems aren't over: several Tholian ships are approaching. Using continuous streams of energy, the Tholian vessels form a complex web that completely surrounds Enterprise. As the web closes in on the ship, Forrest tries to fight back, but to no avail. Desperate, he orders everyone to abandon ship. From the bridge of the Defiant, Archer and his team watch in shock as Enterprise explodes with Forrest onboard.