The Special Affairs Agency was founded in 1951, to manage federal law enforcement and national security issues as they were affected by paranormal activity. SAA (more commonly referred to as "the Agency," despite being named a "Department" in 1972) was formed by a merger of four existing agencies: the Treasury Department's Special Enforcement Service, the CIA's Directorate of Unconventional Studies, the State Department's Special Research Office, and the Pentagon's Joint Services Global Meteorological Survey Office.

DSA's existence has always been public, but its exact mission specifications are classified. Its existence appears in no official government documents outside of its formation in the First Amendment of the National Security Act (itself classified until 1982). DSA derives its budget from various "black project" appropriations and covert licensing of advanced technology through "cutout" corporations.

The government was forced to acknowledge DSA's existence and mission after the Medicine Bow Incident. In the spring of 1958, DSA agents operating out of the Colorado Springs Field Office became aware of a high level of extraterrestrial activity on the Colorado-Wyoming border. The investigation uncovered a large-scale "harvesting" operation being conducted by Greys. The aliens' advance base, located in Medicine Bow National Forest, was pinpointed after the entire population of Casper was abducted in a single night. Two civilians escaped and contacted military authorities, who in turn alerted the DSA. On the night of August 18, DSA agents led local law enforcement authorities and an infantry company of the Wyoming National Guard in an assault on the base. During the engagement, an antimatter power source's containment catastrophically failed, resulting in an estimated 3.5-megaton explosion.

A cover-up was impossible, given the magnitude of the blast and its secondary EMP effects. On August 20, President Eisenhower revealed to the world the history of American conflict with extraterrestrials since the 1947 shoot-down of a Grey reconnaissance craft at Roswell. Eisenhower's speech marked the beginning of the world's mass admission of supernatural activity: within a week, over half the nations on the planet had at least tentatively addressed the issues of magic, psychic powers, nonhuman intelligence, or alien visitors in a public forum. Contrary to the expectations of many sociologists, upheaval was surprisingly mild: these revelations merely legitimized beliefs that millions of people had previously been ashamed to hold.

Today, DSA is one of the world's foremost government organizations dedicated to protecting humanity from paranormal threats. The Agency is headquartered in Kansas City, MO, with 10 additional field offices and several hidden facilities in the United States. The State Department also hosts DSA liaison offices in over 20 nations. DSA employs an estimated 1,800 Special Agents, plus over 11,000 other personnel in various clerical, maintenance, scientific, medical, investigative, logistical, and security roles. Exact details of the Agency's personnel roster are classified for the protection of its agents.

DSA is officially limited to operations within the United States. However, the Agency has reciprocity agreements with the governments of Canada, the United Kingdom, Australia, Japan, the Philippines, and South Africa, which allow DSA agents to operate in those nations with the supervision of local counterpart agencies. Hong Kong was a partner until the end of local British rule, but its status is currently under negotiation with the Chinese government. DSA personnel have also been seconded to the United Nations and NATO for various operations.

Although the DSA's existence is known to the world at large, it does not maintain a public face (with the exception of a handful of public affairs agents from the Administrative Directorate). DSA agents and employees are usually drawn from other federal or state agencies, and officially maintain their previous positions. If such a cover would compromise an employee's identity, or if he has no previous government service from which to draw a cover, he is issued a government ID for another agency with facilities in his cities of residence. DSA facilities are not marked as such and are guarded by personnel in private security uniforms. An entire subset of conspiracy theory has sprung up around identifying DSA personnel and offices, despite the fact that knowingly breaching a DSA agent's cover carries a federal charge of obstruction of justice.