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MAJOR SPOILERS
WARNING! This article contains MAJOR spoilers for the recently released novel Available Light. Caution is advised.

The Federation Security Agency or FSA was the civilian intelligence and law enforcement agency of the United Federation of Planets. (TOS movie: Star Trek III: The Search for Spock, TOS comics: "Old Loyalties", "Finnegan's Wake", DS9 - Typhon Pact novel: Zero Sum Game, TNG - Cold Equations novel: Silent Weapons)

In this capacity, the FSA collected and correlated political, military and social information on foreign governments. These specialists typically acted in information processing roles, however, they were also known to have performed counter-intelligence duties. (FASA RPG module: The Federation) The FSA's military counterpart was Starfleet Intelligence. (DS9 - Typhon Pact novel: Zero Sum Game)

In the 2260's, the organization was concerned about threats from Vulcans against Memory Prime after they learned that one of the Adepts of T'Pel had been hired for a contract against a target on the planetoid installation. (TOS novel: Memory Prime)

The TOS novel Memory Prime identifies the organization as the "Federation Security Service" during the 2260s.

In 2285, an operative of the FSA took Doctor Leonard McCoy into custody after McCoy began exhibiting erratic behavior due to his experience with Project Genesis and Spock's katra. The operative, who identified himself as "Federation Security", warned McCoy not to discuss Genesis in public, and after McCoy clumsily attempted a Vulcan nerve pinch, told him that "you're going to get a nice long rest, Doctor." (TOS movie, novelization & comic adaptation: The Search for Spock)

The operative who takes McCoy into custody in the bar, in Star Trek III: The Search for Spock, identifies himself as "Federation Security". It is likely that this is the same organization.

Situations where Starfleet personnel were the subjects of criminal investigations or were victims of crimes committed by other Federation citizens were Federation Security Legion matters. This detail of Federation Security was tasked with investigating such occurrences. In particular, it was mandatory for the Legion to begin investigations when any sort of assault against a Starfleet captain was made by another member of the service. James T. Kirk disliked these investigations, finding the Legion to be paranoid and overly suspicious.

Federation Security members Sean Finnegan and Heather Van Horne, both Legionnaires, were sent to Omicron Ceti to investigate the deaths of the crew of the USS Zephyr and several landing party personnel from the USS Enterprise-A. They were then diverted to the Enterprise herself after it was reported that William Bearclaw had made an attempt on the life of Captain Kirk. (TOS comic: "Old Loyalties")

In some of Federation Security's appearances, most notably in the comics, operatives such as Sean Finnegan wear Starfleet uniforms. However, they still identify themselves as Federation Security.

From 2381 on, an elite division of FSA known as the Protection Detail was also responsible for a unique duty: Guarding the safety of the President of the United Federation of Planets. (TNG - Cold Equations novel: Silent Weapons, ST - Destiny novel: Mere Mortals) Prior to its formation, the primary responsibility of protecting the Federation President fell to the authority of Starfleet Security.

At one point, the FSA was headed by the High Commissioner of the Federation Security Council. (FASA RPG module: The Federation) By 2382, its leader was known as the Federation Security Agency Director. That same year, Rujat Suwadi of Zakdorn served as FSA Director. Later that year, he was called to a high-level meeting with Federation President Nanietta Bacco at the Château Thelian after a Typhon Pact spy successfully stole classified data on the Federation Starfleet's slipstream drive system from the Utopia Planitia Fleet Yards in orbit of Mars. (DS9 - Typhon Pact novel: Zero Sum Game)

As one of the Federation's primary law enforcement organizations, the Federation Security Agency operated a fleet of interceptors which was crewed by officers and empowered to enforce Federation law in its territory. In 2384, one of its interceptors, the Sirriam, was destroyed by the Breen Militia during a routine patrol of the Komatsu sector. Later that year, the FSA took several losses after successfully preventing two assassination attempts on President Bacco by the Breen Confederacy, who was in the midst of conducting secret talks with Imperator Sozzerozs of the Gorn on Orion. (TNG - Cold Equations novel: Silent Weapons)

In 2385, during the brief secession of Andoria from the Federation during the Andorian Fertility Crisis, the FSA was responsible for collecting intelligence regarding the involvement of the Typhon Pact, specifically the Tholian Assembly in Andorian affairs. (ST - Typhon Pact novel: A Ceremony of Losses)

Following the deactivation of the Uraei surveillance program and exposure of Section 31 to the public in 2386, the FSA was tasked with bringing many of its top operatives and assets to justice and keeping them in custody until trials could be held. Most Section 31 operatives were held at the FSA Detention Facility in San Francisco. Individuals included Admiral Edward Jellico, Alynna Nechayev, and Tujiro Nakamura.

Among the arrestees was Admiral William Ross. He was murdered by FSA agent Margo Dempsey in retaliation for the death of her husband Clark in a shuttle crash which had been engineered by Section 31 to assassinate a Federation diplomat. The FSA and Starfleet later determined that following her husband's death, Dempsey had taken steps to ensure that the information did not show up in any of the background investigations the FSA conducted of agents who would be guarding Section 31 operatives taken into custody. Following Ross' death, the FSA worked with Starfleet to revamp its procedures, with anyone who would be coming in contact with those Section 31 operatives subjected to complete background checks. Furthermore, the list of people approved to have contact with these operatives was limited and required approval from top officials in the Federation government. (TNG novel: Available Light)

Based on the duties and responsibilites of the organization, the Federation Security Agency is comparable to real-life organizations such as the United States Secret Service, which is tasked with protecting the nation's leaders. As well as the United Kingdom's Security Service (MI5), and the United States Federal Bureau of Investigation (FBI); both of which are tasked with domestic intelligence and security operations.
It appears that the organization has gone through several name changes during its existence. As the TOS novel Memory Prime lists it as the "Federation Security Service" in the 2260s, the "Federation Security Legion" in the 2280s, and finally the "Federation Security Agency" by the 2380s. This is not dissimilar to the United States Federal Bureau of Investigation (FBI) which was originally established as the Bureau of Investigation (BOI) in 1908, before it changed its name to the United States Bureau of Investigation (USBI) in 1932, and eventually to its current name Federal Bureau of Investigation (FBI) in 1935.

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