The Secret Empire was originally created as a criminal enterprise designed to help fund HYDRA. It eventually developed into its own separate organization.It occasionally utilized superhuman operatives, and even financed the creation of their own mercenary, Boomerang. This incarnation came into frequent conflict with the Hulk.
One incarnation of the group inserted operatives in White House administrative roles, and framed Captain America for murder. During this same period, the organization began a significant campaign against mutants, capturing members of both the X-Men and their foes, like the Blob and Unus the Untouchable. This iteration of the Empire fell after Captain America defeated their operative, Moonstone, and their White House connection committed suicide. However, these events led Steve Rogers to experience a philosophical schism which briefly led to him abandoning the identity of Captain America to become Nomad.
A later version of this group also came into conflict with Captain America, as well as the Defenders and other heroes. This incarnation of the Secret Empire, led by Professor Power, abandoned the numbered cloaks worn by members of previous incarnations in favor of dressing like Roman centurions. It also used superhuman agents, like Mad Dog and the Mutant Force. The Defenders ultimately defeated this group and Professor Power was rendered comatose.
Despite the frequent failures that groups using the name experience, the Secret Empire continues to rise to threaten the Marvel Universe.
The Secret Empire was created by Stan Lee and Jack Kirby. It first appeared in Tales to Astonish #81 (1966).