The Secret Empire is a subversive organization concerned with conquering the U.S.A. through surreptitious means such as forming underground armies and engaging in deeply layered conspiracies. Traditionally, the Secret Empire has been organized by code numbers given to each member which indicates their rank within the organization. The nine highest-ranking members originally comprised the Council of Nine to provide direction for the rest of the organization, while the person who held the rank of Number One served as the supreme leader. (The original Secret Empire was funded by the terrorist group Hydra, and its underground branch called THEM made the Empire a branch of Hydra alongside its own scientific division, A.I.M. Later iterations of the Empire were completely self-sufficient.)
One of the Empire's earliest known overt actions involved the attempted theft of the U.S. Air Force's Orion Missile, for which they hired the mercenary Boomerang, although he was thwarted by the Hulk. At the same time, S.H.I.E.L.D. agent Gabriel Jones had infiltrated the Council of Nine in the guise of Number Nine, and he killed all of the Council except for Number One himself. Later, fleeing the Hulk, Number One's robes caught in the door, keeping him from escaping an explosion he had planned for his enemies, and he was killed. Ironically, his body was rendered unidentifiable by the blast, leaving the man who sought fame to be buried as a "John Doe."
A subsequent Number One, an unidentified U.S. government official, turned the Secret Empire's attention to the Brand Corporation. At the time, the Beast was a Brand employee, and his research made him a target of numerous Secret Empire agents, including the Brotherhood of Evil Mutants, the robot Quasimodo and the Griffin. At the same time, Number One plotted to topple the U.S. government. Among their plots, using a front organization called the Committee to Regain America's Principles, they promoted their agent Moonstone (Lloyd Bloch) to the public as a super-hero, framed Captain America for the murder of the Tumbler, and captured mutants of the X-Men and the Brotherhood of Mutants. The cumulating of these plans came when Number One used the captured mutants' mental energy to power his command ship, landing on the White House lawn, and demanding the U.S.'s surrender. Captain America, the Falcon and the X-Men opposed the Secret Empire. Seeing his plans falling to ruin, Number One fled into the White House, pursued by Captain America. Removing Number One's hood as they fought, Captain America was shocked when he recognized Number One's true identity. Number One then committed suicide rather than be imprisoned.(Recognizing Number One from his prestigious political position, Captain America became so shaken and disillusion that he temporarilty retired his heroic identity to become Nomad.)
Professor Power created a Secret Empire consisted of wealthy and powerful men from the worlds of politics, religion, espionage, military big business and the mass media. His followers even included former agents of S.H.I.E.L.D., such as the superhuman Leviathan (later Gargantua), and assimilated part of Roxxon Oil's Nth Command project into their resources. They also employed the superhumans Mad-Dog, Mutant Force, Harridan, Cloud and Seraph. The Defenders discovered Power's scheme of using a satellite with mind control technology that would force countries into engaging in war with each other so that once the Earth's arsenals were depleted, the Secret Empire would rule over what was left. Originally captured, they escaped with the help of Seraph and Cloud and prevented the launch of the satellite.
The Secret Empire became one of the many criminal organizations funded by the Red Skull, but was left largely to its own agenda. Reorganized by their new Number One, the Secret Empire expanded their inner circle to a Council of Ten, and the thousands of members who comprised the outer circle believed themselves to be merely members of a fraternity. All of the outer circle agents helped prevent the Secret Empire's operations from being traced back to the inner circle. The most extreme members of the outer circle were the Pretorians, a fanatical motorcycle gang of white supremacists led by the maniacal Chainsaw. During this time, Moon Knight teamed with Spider-Man and the Punisher to thwart the Empire's attempt at launching Skyclaw, a satellite which would have been capable of destroying other satellites in orbit. Moon Knight would later be have to take down Midnight, his former sidekick, who had become twisted into a Secret Empire agent.
When the Viper (Madame Hydra) took over leadership of the Secret Empire, she used two special agents, Trickshot and Javelynn, to help train the genetic engineering experiments called "Bio-Coms" (biological combat units) in order to sell them as warriors. Hawkeye discovered their base, befriending an escaped Bio-Com that he named "Rover," and with War Machine, brought down the Empire with the help of Trickshot turning on the Viper.
Following this, the Royalist Forces of America organization adopted the Secret Empire's name. Led by William Taurey, a descendant of Loyalists from the American Revolutionary War, the Elite of the Royalists believed themselves to be eugenically superior to other Americans. To gain followers, the Imperial Forces would present themselves to working-class Americans as supporters of the disenfranchised who would help them gain power and respect. Many of their recruits were indoctrinated to serve the Elite's interests. The Empire also used Arnim Zola to create genetically-modified superhuman agents, ultimately creating Brute Force and Charcoal. Scientist Hesperus Chadwick also designed the Shriequencer, a sonic weapon they intended to use to eradicate the U.S. government.
When the Imperial Forces came to Burton Canyon, Colorado, to collect townspeople for experiments, they were opposed by the Thunderbolts. Charcoal left the Imperial Forces to join the Thunderbolts, and with the heroes' help, infiltrated the Imperial Forces at a recruitment drive but became embroilled in a "Kill Derby," forcing them to engage in combat with their Shocktroopers (elite guards) and Brute Force for the entertainment of their followers. However, the Imperial Forces' Cornwallis base was invaded by Citizen V (Dallas Riordan), and she summoned the Jury, led by U.S. Agent, who were then trying to arrest the Thunderbolts. While the other heroes fought off Brute Force, Citizen V destroyed Chadwick's Shriequencer and took him captive. Taurey turned to Baron Zemo for aid, but Zemo refused, and Taurey was forced to abandon Cornwallis.
Later on, the Secret Empire became interested in a chemical cryogenic compound being developed at the Bryar chemical plant in Burton Canyon. Charcoal's father Calvin Burlingame was dispatched to convince him to rejoin the Empire and aid his father in stealing the compound, but Charcoal refused and fought his father and Imperial Forces agents at the plant. During the fight, Calvin Burlingame was knocked over the vat containing the compound. Charcoal had an opportunity to save him, but ultimately chose to do nothing, and Calvin fell into the compound. It is not clear whether the compound killed him or not. The Elite remain the masters of the Secret Empire.