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Starfleet Intelligence (SI) was the primary intelligence gathering and covert operations branch of both the United Earth Starfleet and the United Federation of Planets Starfleet that followed.
SI first came into existence after United Earth founded Starfleet in the 2140s. As humanity began to branch out into the galaxy with the development of faster warp engines, SI had to deal with a number of external threats such as the Klingons. In addition, SI also had to deal with internal threats as well, such as the extremist group Terra Prime which wanted to expel all aliens from the Sol system, and the rogue intelligence agency Section 31. During the 2150s Gannet Brooks was an agent within the organization and played a key role in bringing down Terra Prime before it could destroy Starfleet headquarters.
After the founding of the Federation SI became part of the Federation Starfleet. Like it did when it was a branch of the UE Starfleet, SI continued dealing with external threats such as the Klingons, Romulans and various other groups.
During the late 23rd century, Elias Vaughn joined SI after graduating from the academy and finding he had a talent for intelligence. At first working as a low-level intelligence analyst on Earth, Vaughn was eventually able to become a field operative, and worked for the next 80 years as an operative. On one of his first missions he helped short circuit a Romulan Tal-Shiar plot to destabilize the new Klingon-Federation alliance and keep Qo'noS from being further damaged. As the Cardassians became more of a threat in the 24th century, Vaughn worked on a number of assignments dealing with that new threat. Following the conclusion of the Dominion War, Vaughn decided to pursue his love of exploration and transferred from intelligence to command.
Also in the late 23rd century, SI also approached Nyota Uhura and recruited her into the organization after the successful opening session of the Khitomer talks. At first passing on public information she came across during her work, including command of her own ship, Uhura became more and more involved in SI. By the 2350s Uhura was an Admiral and the head of SI. She would remain as SI's head into the 2370s, at which point she was over 130 years old.
Rogue operatives in SI developed and tested a phasing cloak in the 2350s. When the existence of the cloak was exposed by Commander William Riker, Starfleet court martialed Admiral Erik Pressman and several other officers attached to SI.
SI was quite active in the 2360s and 2370s as war with the Dominion became inevitable. One of their greatest failures occurred during the war, when they failed to detect a Dominion fleet that invaded and occupied Betazed.
By 2401, Worf was working with SI. He described himself as a "sub-contractor" for SI, and was working as a handler for Raffi Musiker, who was working on an undercover assignment to determine who had stolen weapons from the Daystrom Institute. Worf had been informed by Odo that a renegade faction of Changelings had broken away from the Great Link and were looking to take revenge on the Alpha Quadrant powers for their loss in the Dominion War. SI and Starfleet elected to keep the news quite as they feared letting it out would spark another conflict with the Dominion. After rescuing Raffi from the Ferengi Sneed, the pair captured Titus Rikka, who had extensive underworld contacts. He turned out to be one of the renegade Changelings. After Worf was forced to kill Rikka, he and Raffi became partners in order to defeat the renegades before they could attack Starfleet.