As the species of the Alpha and Beta Quadrants developed, they often created governments
and militaries to oversee and protect their economic and political interests.
Yet as civilizations progressed and interacted there also grew a need for intelligence agencies,
to provide vital information about enemies, allies and even their own people.
And so by the 24th century, many of the greatest powers in the region were known to employ
clandestine groups such as the Tal Shiar of the Romulan Star Empire, the Obsidian Order
of the Cardassian Union, and Klingon Intelligence for the Klingon Empire.
And while the United Federation of Planets had Starfleet Intelligence, they had to abide
by a strict legal code, and were nowhere near as feared or infamous as the other organizations,
which used torture, kidnapping and any other means necessary to accomplish their missions.
Thoughout the region, the United Federation of planets was known as an alliance of systems
based on mutual respect and trust, embracing democracy, equality and individual freedom,
while still working within a responsible and fair legal system.
However in truth, Starfleet, the military and scientific arm of the Federation, had
their own secret intelligence operation working entirely in the shadows, able to act outside
the law and without oversight, accountable to no one.
Section 31 as they were known, existed since the founding of Starfleet, getting their name
and mandate from Article 14 Section 31 of the Starfleet Charter, which allowed for extreme
measures to be taken in times of crisis.
They then interpreted this passage to mean they could do whatever was necessary to accomplish
their objective without limitations, just like the other known agencies of the region.
However, in their own way, Section 31 also believed deeply in the principles of the Federation,
and did not act out of malice or a need for self-preservation, willing to die for the
cause and taking no actions against those who might threaten to expose or work against
them, so long as they did not interfere with any active mission.
During the mid 22nd century, before the formation of the Federation, Section 31 recruited Malcom
Reed, a promising young Starfleet Officer who at first believed he was doing the right
thing, but grew uneasy about their methods, attempting to retire in the 2150s, still early
on in his career.
However agents of Section 31 were not normally allowed to retire completely, able to be called
into active service at any time.
Such was the case in 2154, when a high level operative named Harris contacted Malcom Reed
who was serving aboard the Starship Enterprise NX-01, under Captain Jonathan Archer.
At the time the Enterprise was investigating the disappearance of Phlox, their highly skilled
Denobulan doctor, who had been captured by the Klingons so he might develop a cure for
a terrible disease that risked spreading throughout the Empire.
Harris then explained to Reed, that it was in the best interest of the Federation for
the Klingons to find the cure in order to ensure the Empire remained stable, and did
not descend into chaos and war which might spread beyond their borders.
Understanding the gravity of the situation, Reed reluctantly agreed to help Section 31
by slowing down the progress of Captain Archer’s investigation, giving Phlox as much time as
possible to find a cure.
However Reed was eventually caught and arrested, revealing the true nature of his mission and
so the Enterprise did what they could to help, allowing for Phlox to create the cure that
was desperately needed.
After this incident Reed could no longer abide having his loyalties divided, and so informed
Harris he was no longer taking orders from Section 31.
However, just a year later in 2155, when inter-species peace talks on Earth were being threatened
by Terra Prime, a xenophobic terrorist organization that wanted all aliens gone from the system,
Malcom Reed had to contact Harris asking for help from Section 31 to stop the terrorist
attack.
Harris agreed to give the necessary information, thereby placing Reed in his debt, able to
be called once more to serve the agency if needed.
After the formation of the Federation in 2161, Section 31 continued to work in the shadows,
doing whatever was necessary to protect the growing alliance, covertly aiding them both
in times of peace and war.
In the 2250s, following the devastating conflict between the Klingons and Federation, Section
31 sent an agent to meet and recruit Phillipa Georgiou, the former ruler of the Terran Empire
in the mirror Universe, who was transported to a new reality where she temporarily served
aboard the starship Discovery, using morally questionable tactics to help the Federation
defeat the Klingon threat.
Over a century later in 2374, Section 31 recruited Doctor Julian Bashir, the genetically enhanced
chief medical officer aboard Deep Space nine.
In order to ensure his loyalty to the Federation, he underwent intense psychological testing,
placed in a situation where he was meant to believe he was a traitor working for the Dominion,
the Gamma Quadrant super power which allied with the Cardassian Union to invade the Alpha
Quadrant.
However no matter what was said to him, or how much evidence was given, Bashir refused
to believe it, and continued to be loyal to the Federation.
Passing the test, the Section 31 operative Luther Sloan welcomed Bashir into the organization,
despite the doctor’s clear objections and concerns.
After Sloan departed, Bashir went directly to his commanding officer Benjamin Sisko and
revealed all that had occurred.
Sisko then ordered to Bashir to play along with whatever Sloan wanted, so he might become
a double agent, learning all he could about this mysterious organization.
The following year, with the Dominion war continuing to create chaos in the region,
Sloan re-appeared to give Bashir his first assignment, sending him to a Federation-Romulan
conference on Romulus where he would act as a spy alongside his Section 31 contact, who
posed as a human cartographer named Wendell Greer.
Bashir agreed to participate in the mission in order to learn what Section 31 was doing
and expose them as an illegal clandestine organization.
However Sloan was well aware of Bashir’s true loyalties, and manipulated the situation
to trick the doctor into working with the Romulan Senator Kimara Cretak to access Senator
Koval's personal database, believing he had been targeted for assassination by Section
31.
Although Koval was a political rival to Cretak, she was truly loyal to Romulus and would not
allow one of her own people to be killed by an outside organization.
However they were soon apprehended by the Romulan government who arrested and imprisoned
Cretak, accusing her of treason for working with a Federation Officer.
Bashir then learned that he had been duped, and that the plan all along was to eliminate
Senator Cretak so that Koval could take power on Romulus, as he was actually an agent for
Section 31 who could be trusted to serve the best interests of the federation.
By placing an agent so high up in the Romulan government, they not only ensured that the
alliance against the Dominion remained intact, but were well positioned for after the conflict
was won, as both the Klingon empire and Cardassian Union would be severely weakened, leaving
only the Federation and Romulan Star Empire as significant super powers, which might one
day go to war.
Bashir also learned that Admiral Ross of Starfleet, a man he had trusted, knew about Section 31
all along, and while he was not a part of the organization, he sometimes worked with
them to advance the interests of the Federation.
During the final months of the Dominion War, Bashir discovered that Section 31 was behind
the Morphogenic virus threatening to destroy the Founders, rulers of the Dominion.
Although it was the Founders who initiated the war, Bashir could not stand by while the
Federation committed genocide against an entire species, and so with the help of his friend
chief engineer miles o’brien, they extracted the cure from the mind of Luther Sloan, who
attempted to kill himself to prevent the information from falling into enemy hands.
And while Bashir was successful in his mission, the Federation council ultimately chose not
to give the cure to the Dominion, as they felt it would only strengthen the enemy during
a time of war.
In the end this proved to be a wise decision, as Odo, a changeling working with the federation
Alliance was able to use the cure to negotiate a peace treaty after the battle of Cardassia,
ensuring victory for the Alpha and Beta Quadrant forces.