The Secret Empire is a fictional organization appearing in American comic books published by Marvel Comics. They first appeared in Tales to Astonish #81 and were created by Stan Lee and Jack Kirby. They were originally a branch of Hydra but later became a separate independent group.

They made their debut in the Marvel Cinematic Universe as a major antagonist in season 2 of Agent Carter. Under this incarnation, they are named the Council of Nine.

The Secret Empire first appeared in Tales to Astonish #81 and was created by Stan Lee and Jack Kirby.

This subversive organization has been headed by a number of different leaders, always known as "Number One", with each iteration's goals following the desires of its current leader. The Secret Empire was founded by a scientist who felt like an anonymous nobody. The organization began as a criminal enterprise, a subsidiary of Hydra, which provided it with financial support. The Secret Empire served to distract the attention of authorities, such as S.H.I.E.L.D., from Hydra's activities, although the original Number One sought to break away from Hydra. The Secret Empire hired the mercenary Boomerang to steal plans for the Air Force's Orion Missile, but he was defeated by the Hulk. In attempting to blow up the Hulk, Number One instead killed himself.

Some time later, the organization regrouped under a new Number One. This Secret Empire infiltrated Roxxon Oil's Brand Corporation, tried to ruin Captain America's reputation, and kidnapped several mutants—specifically Havok, Polaris, Beast, Iceman, Angel, Mastermind, Mesmero, Blob and Unus the Untouchable—to harness their energy to power a "flying saucer". Number One landed the saucer on the White House lawn, and, after defeating the Empire's "replacement" hero—the first Moonstone—demanded the government surrender control to him or he would detonate nukes in every major American city. The Secret Empire was defeated by Captain America, Cyclops, the Falcon, and Marvel Girl, and Captain America pursued Number One into the White House. Rather than face capture, Number One unmasked himself, then committed suicide. The leader of the Secret Empire was revealed to be a very high U.S. government official attempting a coup d'état. Although his identity and face are never revealed to the reader, it is strongly implied in the dialogue that Number One was the President of the United States. The government covered up his guilt and suicide with the help of a double. This led to Captain America giving up his role for a while and taking on the role of Nomad. The story was first published in 1973, when the sitting president was Richard Nixon, embroiled at the time in the Watergate scandal. Writer Steve Englehart specifically intended this issue as a metaphor of the Watergate case and the Nixon era.

Later, Professor Power became the new Number One. He sought to trigger a nuclear war between the U.S. and the Soviet Union. The Defenders defeated Professor Power and the Secret Empire, as well as their agents Mad Dog and Mutant Force.

Gabe Jones, agent of S.H.I.E.L.D., is assigned by Nick Fury to infiltrate the group in an attempt to bring it down.

The Secret Empire also sought to eliminate Moon Knight, who they believed had disrupted some of their operations. The real guilty party was Moon Knight's sidekick Midnight and when Moon Knight and his sidekick confronted the Secret Empire, Midnight was hit by an energy blast from the group's new leader, the mysterious Number 7. Moon Knight abandoned his sidekick, believing that he was dead, but in truth he was still alive, though horrifically disfigured and maimed. Number 7 ordered Midnight to be transformed into a cyborg, driven by his hatred for Moon Knight (for being abandoned by his mentor) as well as a mechanical failsafe that caused him to suffer intense pain if he disobeyed Number 7.