Starfleet Intelligence is the information gathering section of Starfleet and is responsible for foreign and domestic espionage, counter-espionage, and the identification of external security threats. It is modeled on the classic intelligence agencies of Earth’s past (CIA, MI6, etc.)
The Starfleet Intelligence Agency is divided into seven different directorates: analytics corps, clandestine services, internal affairs, liaison corps, security section, technical operations, and temporal investigations. There are also subsections crossing over into other departments of Starfleet Command, most notably JAG, communications and security. It is headed by a Command Council of eight members: the Chief Director of Starfleet Intelligence and the directors from each division.
Formal ranks amongst the members of the Starfleet Intelligence Directorate's Council do not apply when thinking in terms of the command structure. Rather, the pecking order is determined through the leadership direction the Chief Director decides to take and, consequently, the department or operation to which each sub-director belongs.
There are seven directorates in Starfleet Intelligence: the analytical corps, clandestine operations, internal affairs, liaison's corps, intelligence security section, technical operations, and temporal investigations. Each has a chief director who oversees all divisional activity, and the directors sit on an advisory board under the Director of Starfleet Intelligence.
Each fleet has an intelligence department, which includes individuals from the primary divisions: the analytical corps, clandestine operations, the liaison's corps and technical operations. In most cases, these departments are based in the fleet's home port, but for the larger, front-lines or deep-space focused fleets, notably the first, third, ninth and twelfth, the intelligence department is based on the flagship (the USS Galaxy, the USS Enterprise, the USS Corinthian and the USS Miranda). Each fleet has a divisional chief in each of the key directorates.
Security section is based primarily in high-clearance locations, especially top-secret holding facilities. They are rarely based on-ship or in the fleet proper. Internal affairs and temporal investigations are both based in San Fransisco, with smaller divisions on the largest star bases or fleet home ports.
The Analysts are vital to the success of the intelligence program. They are responsible for taking the information gathered by Clandestine Field Operatives, interpreting it, and coming up with recommendations to put the information to the best use. Their recommendations are then relayed through the system and distributed to ship-based officers on the front lines who are able to present the information to the commander of the ship's intelligence attachment and up through to the ship's COs. Analysts make up the 65% of the total Starfleet Intelligence population.
Analysts work in various subgroups including political reconnaissance for both foreign and domestic groups, counter-terrorism, translation, media analysis, etc. Most analysts are based at Intelligence Headquarters in San Francisco and London, on high-traffic starbases, and on important tactical stations. Each sub-group has a Secretary that is involved directly with the Command Council of SI, along with the Fleet Director and the Director of the Corps.
The larger ship-based operations on front-lines and flagship vessels have a significant analyst population, and they often take over many of the duties held by liaison corps officers on smaller vessels.
Clandestine Ops are the people in the field gathering information and risking their lives. The command chain of the Clandestine Ops division is different from the others in order to ensure highest secrecy. All missions related activity is conducted through the Director of Clandestine Operations (DCO), the only fully covert position on the Directorates Council.
There are about 400 agents in Clandestine Ops, making up approximately 6% of the Intelligence community. Those 400 are divided according to a 1 through 9 Field Rating, which is determined through time served, rigorous training, and testing of various types: psychological, strength, agility and, for lack of better term, ability for deception. One is the highest attainable rating and held by only a dozen agents usually assigned to deep immersion, undercover field missions that can last years. Most operatives maintain a rating of 4 or 5 for the duration of their careers. In order to become a Clandestine Services Operative, one must undergo strenuous training at Starfleet’s London campus, called 'The Camp', which will provide an initial field rating. Depending upon performance, interest and specialization, the agent-applicant may be offered deep-immersion field training, usually comprising of a year post-Academy and conducted off-site.
Below the DCO, the Clandestine Service hierarchy is organized by operations desk, determined by area of expertise and generally noted via thematic field names. These desks include the 'Green House', the 'Aviary', the 'Parthenon', and the 'Farm'. Each team is organized into two primary categories: handlers and agents. Handlers are rated field agents who have established themselves through years of service. They head agent teams on the field, coordinate missions, and ensure the safety of those involved. The Handlers communicate directly with the Division Director, and often work with the Analytical Corps as well; they might also be analysts who have had extensive field training. In this case, they are technically part of the analytical corps, though if there is a discrepancy they are expected to work within the CS command structure.
Clandestine Operations works closely with all other directorates within the intelligence community, but are most closely tied to the analytical and liaisons corps.
Internal Affairs often work with the JAG Corps or in conjuncture with Clandestine agents. I.A. is responsible for investigating higher-ranked officers within the context of sensitive situations: monitoring the actions of suspect captains in a starship setting, admirals or ambassadors planet-side, etc. Officers monitored by I.A. might be thought to be abusing their rank and privilege, working with potential enemies of the state, or responsible for intelligence leaks; they may also be suspected as enemy espionage agents. Depending on the situation and evidence already collected, Clandestine Operatives may be requisitioned for a coordinated and long-running infiltration. I.A. is also used to monitor Captains new to command through undercover agents (often younger or less experienced agents on loan through Clandestine Ops) in order for Starfleet to best establish a thorough competency report and command profile.
The Liaisons are the visible component, serving as a direct link between the rest of the Fleet and SI. Liaisons are stationed at embassies, on ships, and often accompany diplomatic teams. Embassy liaisons are field rated 9, with higher security clearance; they are never intended to be in the field except in the most extraordinary of circumstances. Ship based liaisons are often between and 6 and 8, depending upon the ship: their security clearance is high and they are able to react to situations in the field, but are rarely sent planet side or into deep cover missions unless absolutely necessary.
The hierarchy of the Liaison’s Office is fairly complex. Underneath the Director are Chief Liaisons for each Fleet; depending on the size of the Fleet and the types of ships under its command (more ships of the line increases the number of agents stationed within the Fleet), the Chief Liaison could have between 6 and 30 agents under him. Liaison agents are stationed on exploratory and conflict (front lines) ships. Ship-based liaison officers report directly to the Fleet’s Chief Liaison, who reports directly to the Director. They are under the ship’s command structure to a point -- orders from the ship’s Captain will be followed unless the orders from the Fleet's Chief Liaison are contradictory.
For flagships, the liaison corps has a much smaller footprint and much of the duties a liaison officer would commonly fulfill are consumer by analysts in the larger operations.
Tech Ops is in charge of the technological aspects of intelligence operations. They work to construct implements to suit each specific mission and situation. They are the stereotypical egg-head geek types, a combination between scientist, engineer, and magician. They keep Starfleet Intelligence on the cusp of the latest technology, much of which is highly classified. They are also responsible for keeping abreast of technological developments across the quadrant, policing illegal technologies, and assuring the enforcement of treaties. They are commonly stations at headquarters and aboard significant outposts throughout the Federation. With the exception of flagship intelligence command centres, however, they are rarely ship-based.
This small organization within the intelligence community largely keeps to itself. Their official orders are to maintain the timeline and investigate any incidences of time travel by Federation citizens that may have an effect on the time line. How they do this and the extent to which they are able to monitor the time line is vague.