Jonathan Archer was the villainous protagonist of the Star Trek: Enterprise two-part story "In A Mirror, Darkly". He was the mirror universe counterpart of Jonathan Archer, captain of the Enterprise NX-01 in the prime Star Trek universe. The polar opposite of the prime Archer, the mirror Archer was a ruthless soldier of the Terran Empire. He believed that it was Humanity's destiny to to conquer all other races and rule the galaxy, even harbouring ideas of seizing such power for himself. He was portrayed by Scott Bakula.
Archer was originally in line to command the ISS Enterprise himself, but Captain Forrest assumed command instead. Archer would later insist that this change of command was the result of an unspecified number of admirals conspiring against him.
Prior to serving aboard Enterprise, Archer was romantically involved with Hoshi Sato. When Forrest was given captaincy of Enterprise, however, Sato saw an opportunity to advance her career and left Archer to become the captain's consort. Although Archer claimed to understand that Sato leaving him was strictly a career move, he was nonetheless hurt and resentful.
Despite taking away Archer's command and his lover, Forrest selected Archer as his first officer. He later claimed that he trusted Archer because he felt Archer never sought power and glory, and that he had no ambition. But Archer did indeed harbour ambition for his own command, and it was only a matter of time before those ambitions surfaced.
In 2155, after learning that the Tholians had captured an Earth ship from a parallel universe and a century in the future, Archer attempted to convince Forrest of the necessity of capturing the ship and taking advantage of its advanced technology to crush a rebellion that was devastating the Empire. Forrest rebuffed him, however, accusing Archer of attempting to gain favour with the Emperor. In response, Archer staged a mutiny, imprisoning Forrest in the brig and taking command of Enterprise. In addition, Archer took advantage of his new command by rekindling his romance with Sato.
Archer assigned Commander T'Pol as his first officer, and ordered her to help Commander Tucker install a Suliban cloaking device, which they had stored on the ship. Later, Archer captured a member of the Tholian species and tortured it for information on the location of the Earth vessel. Learning that it was being kept in the Vintaak system, Archer set a course, and encrypted the helm controls with a random code. Archer also ordered Sato to send all data on the Earth vessel to Fleet Admiral Gardner, knowing that Gardner would support his plan should Forrest regain control of the ship. This plan proved prescient, as Forrest did indeed regain command of Enterprise, putting Archer in the agony booth for ten hours as punishment for his actions.
Archer's plan worked, however, and Admiral Gardner ordered Forrest to continue Archer's mission. Traveling into Tholian space under cloak, Enterprise arrived in the Vintaak system and located the Earth ship: The USS Defiant. Examining the ship, Forrest ordered Archer to lead a boarding party aboard the Defiant, download the database and destroy the ship. Archer vehemently disagreed with Forrest's decision, stating that they should attempt to take the Defiant with them, but Forrest overruled him.
As Archer led the boarding party, the Tholians discovered Enterprise's presence in their space, and launched an attack. Forrest ordered the crew to abandon ship in the escape pods, while he stayed aboard and attempted to fight the Tholians off long enough to let his crew get away. As Archer and his team watched from the bridge of the Defiant, Enterprise was destroyed with Captain Forrest still aboard.
With the Tholians surrounding them, Archer took control of the Defiant and easily fought them off. Detecting Enterprise's escape pods, Archer ordered them brought aboard, and christened himself captain of the Defiant.
While aboard the Defiant, Archer learned about his counterpart in the other universe. At first, he protested that his counterpart was not a great man but weak and foolish for his efforts in helping to form the United Federation of Planets (which he dismissed as a "Federation of Fools"), noting that great men should conquer other species rather than work together with them. Secretly, however, Archer resented his counterpart and was insanely jealous of his success, particularly when he learned that the other Archer had a long, respected career as a starship captain, diplomat, and statesman; had two planets named for him; and was noted as the "greatest explorer of the 22nd century." His preoccupation with his counterpart's success eventually drove him to have a mental breakdown, taking the form of hallucinations of the other Archer, who mercilessly taunted him about his own inadequacies.
Archer became determined to gain the same respect and hero status accorded to his counterpart. When it was determined that Slar, the Gorn foreman that was employed by the Tholians, was responsible for stealing key engine components and indiscriminately murdering several engineers, Archer rejected T'Pol's advice to negotiate with him. Seeing an opportunity to earn the respect of his crew, he acted on the encouragement of his illusory counterpart and personally led a team of MACOs to the lower decks of the Defiant to seek out and kill Slar. The ill-advised operation resulted in a bloody pyrrhic victory: during the pursuit, Major Malcolm Reed was seriously injured, several other MACOs were killed, and Archer himself nearly died at Slar's hands before ultimately defeating and killing the Gorn.
When the Defiant eventually made it to the battle between Starfleet and rebel forces, the ISS Avenger, under the command of Admiral Black, was the only surviving Starfleet vessel. Archer destroyed all but one of the rebel ships, which he allowed to leave so they would tell other rebels what had transpired. Black was grateful to Archer for both his intervention in the battle and for obtaining the Defiant, and assured Archer he would be promoted at the earliest opportunity. When Archer asked for an immediate battlefield promotion and command of the Defiant on a permanent basis, Black refused, stating he wanted to take the ship back to Earth and have it reverse-engineered to learn about its technology. Archer, fed up with the continuing losses suffered by the Empire, its corrupt leadership, the setbacks his own career was suffering, and the realization that Black would likely take all the credit for his own achievements (all the while being taunted by his illusory counterpart), finally reached his breaking point. In a bold move, he murdered Black and took the Defiant for himself.
In an address before the crews of Avenger and the Defiant, Archer unveiled his most ambitious plan yet: seizing control of the Terran Empire. He argued that the problem with the Empire was its leadership, and publicly announced that he was seeking to make himself Emperor and then stop the rebellion.
In the process of approaching Earth, Archer became more xenophobic in his views, believing they were holding humanity back. In his paranoia, he ordered all alien crew members (with the exception of Doctor Phlox, whom he believed would not be a threat as his species were known pacifists) on the Defiant transferred onto Avenger. Archer later destroyed Avenger as its alien crew, led by Soval, attempted to stop him.
However, as the Defiant was en route to Earth, Archer was betrayed by Sato who, with assistance from Archer's personal guard, Sergeant Travis Mayweather, poisoned Archer and took command. Arriving at Earth, Sato referred to herself as "Empress," and demanded Earth's surrender.