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Starfleet Intelligence focused its efforts on protecting the Federation through covert information gathering, counter espionage, and field operations.
These missions were undertaken by highly-skilled intelligence agents, as well as trusted Starfleet officers who were temporarily recruited for specialized assignments.
Gannet Brooks
"Terra Prime"
A news reporter who had a previous relationship with Travis Mayweather, Gannet Brooks boarded the NX-01 Enterprise under the pretense that she was writing a story about the ship. A security background check revealed that she had made several trips to the lunar colony, leading Captain Archer to suspect she was actually a spy for Terra Prime, a 22nd Century terrorist organization which wanted non-humans to leave Earth.
In reality, Gannet worked for Starfleet Intelligence and had been assigned to identify the real Terra Prime operative who had infiltrated the crew. Gannet warned Travis about the Terra Prime informant, who turned out to be Ensign Masaro.
Captain Picard, Dr. Crusher, and Worf
"Chain of Command, Part I"
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When Starfleet Intelligence caught wind that the Cardassians might have been developing a metagenic weapon — genetically-engineered viruses — which destroy all organic matter while leaving a planet's infrastructure intact, they recruited Captain Picard to assemble a strike team. Picard had conducted experiments on subspace carrier waves, which Intelligence believed was the Cardassians' preferred delivery method for the weapon, so he led the group. The captain selected Dr. Crusher and Worf to accompany him, for their expertise with biotoxins and combat, respectively.
The trio penetrated the suspected Cardassian facility, but the entire metagenic program turned out to be a facade designed to lure the captain of the Federation flagship into a trap. Crusher and Worf barely escaped, but Picard was captured and brought before Gul Madred, who ruthlessly tortured and interrogated Picard in a bid to obtain details about classified Starfleet defense plans.
Admiral Erik Pressman
"The Pegasus"
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According to a report from a Starfleet Intelligence operative embedded in the Romulan High Command, the Romulans had located a piece of wreckage from the U.S.S. Pegasus, Admiral Pressman's former command and a testbed for experimental weapon systems and engines. Now a member of Starfleet Intelligence, Pressman wished to find the Pegasus before the Romulans could salvage its sensitive systems. Unbeknownst to Picard, the admiral had developed an illegal phased cloaking device on the Pegasus, and certain officers in Intelligence wished to restart the project.
The Pegasus had been Riker's first assignment, and he was well aware of Pressman's intentions. Prior to the explosion that caused the Pegasus to disappear, Riker defended Pressman when the rest of the crew mutinied in an attempt to halt the experiment. The experience haunted Riker for years, yet he chose to do the right thing and unveil the cloak's existence to Picard, prompting the captain to have Pressman taken into custody.
Chief O'Brien and Chadwick
"Honor Among Thieves"
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After the Orion Syndicate murdered several operatives, Starfleet Intelligence decided to turn to someone outside of their organization to identify the Syndicate's Federation informant. An intelligence officer named Chadwick brought in Chief O'Brien, as the accomplished engineer who could pose as a resourceful "fix-it" man and ingratiate himself with the Syndicate.
The strategy succeeded and the subject was identified, but O'Brien kept up his subterfuge once the Syndicate allied itself with the Dominion. O'Brien informed Chadwick that the Dominion wanted the Orion organization to assassinate a Klingon ambassador, allowing Starfleet Intelligence to warn the Klingons.
Lasaran
"Change of Heart"
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A Cardassian who supplied Starfleet Intelligence with military secrets during the Dominion War, Lasaran believed the Vorta were becoming suspicious about his behavior and requested an immediate extraction.
Given Lasaran's claim that he could provide vital information about the Founders, Jadzia Dax and Worf took a runabout into Dominion space and proceeded with the risky mission. Unfortunately, Dax suffered a disruptor wound, and Worf opted to retreat and save her life rather than continue on to the meeting with Lasaran, who was later killed by the Dominion.
Koval
"Inter Arma Enim Silent Leges"
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The Chairman of the Romulan Tal Shiar, Koval had been providing Starfleet Intelligence with sensitive Romulan documents for about a year by mid-2375. Publicly opposed to the alliance between his people and the Federation, Koval actually hoped to expand his influence by getting on the Continuing Committee.
At some point, the chairman began working with Section 31, who concocted an elaborate deception that made it seem as if Koval had murdered Vice Admiral Fujisaki, the Deputy Chief of Starfleet Intelligence.
In actuality, Section 31 had manipulated Dr. Bashir to believe this so he would seek help from Senator Cretak, Koval's chief rival. Koval exposed the communication between Bashir and Cretak, undermining Cretak's standing on Romulus and paving the way to Koval's ascension to the Continuing Committee.
