Author's Notes:
This is my own interpretation of Section 31, I know it doesn't necessarily gel with everything we see on screen, or in some cases with established canon.
I have not read any of the expanded universe and don't take them as canon particularly.
I've gone well beyond what we see on-screen, expanding S31 activites during the Dominion War, ascribing inventions and story-events further significance. even positing a reason for Enterprise being a successive name when we never ever see any other ships with Letter suffixes in their names.

I always disliked how Section 31 was portrayed, their existence as a rogue agency within Starfleet Intelligence seemed rather small for their ambition. So I chose to interpret them differently, I think it lends them a certain grandeur.

The Federation's watchful Guardian Devils, quietly making sure the Federation lives up to its dreams.

I hope you all like it!

Section 31: An Unauthorised History

Every race had its secret police, special agents and operatives. Intelligence arms of government.
They held names like The Obsidian Order or The Tal Shiar.
The Federation was no different, Starfleet intelligence was an August body with a history stretching back to the Eugenics Wars and beyond. But they had limits when compared to their opposite numbers in the Romulan or Cardassian Empires.
They had to hold to moral absolutes in line with the rest of the Federation. Their remit was observation, both overt and clandestine. Infiltration was fair game, but overt interference was out.

Section 31 was founded in the earliest days of the Federation. Its founders were formed from concerned members of Starfleet Intelligence and ranking officers of Starfleet Command.
Their goal was simple:
To safeguard the ideals and essential nature of the Federation.
They took their name from the Starfleet Charter, Article 14, Section 31. which allowed for "extraordinary measures to be taken in times of extreme threat".

Section 31's core belief held that the Federation needed to remain pure. Clean handed on the galactic stage. The shared vision of a utopia could not be sullied by the work required to create it.
Section 31's members took it upon themselves to be the Stewards and caretakers of Federation Innocence.
They would shape the federation's neighbours from belligerence into friends, a piece at a time whether they wanted to or not.

Klingons

The chief concern at inception was the burgeoning threat of the Klingon Empire, a considerably more technologically and militarily advanced race than most, possessing such advances as Deflector Shields, Cloaking Technology and Transporters, married to a race which was belligerent and dangerous by any measure that could be applied.
Starfleet could ill afford a war with such a powerful enemy, to that end Section 31's leadership took action with an audacious plan.
Planting operatives within the Empire and manipulating Starfleet officers, they were able to infect the Klingons with a virus.
Initially lethal, the virus was expected to devastate the Empire within months, such a massive drop in Klingon population would make the Empire much more introspective while they built themselves back up to strength. With the Virus being born from their own scientific facilities they would never suspect foul play.
Events did not quite transpire as anticipated as the Klingons reached desperation measures, burning their own worlds to halt the spread and going so far as to kidnap specialist doctors from other races.
In the end, a Cure was created, however it had the unanticipated side-effect of introducing human genetic profiles into the Klingon race at large.
A change which would not be fully reversed for another 150 years.
This alteration would have a profound effect upon Klingon Culture, tempering their more violent urges and stabilising the factional nature of the Empire.

The Enterprise Initiative
As time went on, the Federation formed and Section 31 quietly slipped further into the shadows. They would not resurface for another 200 years.

During this time however, 31 was not idle. The ideals that had initially shaped the burgeoning Federation were ailing,
The threat of the Xindi had made many Federation citizens feel cautious about expanding too quickly into the stars. many questioned whether it was worth doing at all.
Fleets of ships and a hundred colonies had produced a very workmanlike attitude to space and the prevailing attitude was one of introspection and personal development.
Section 31's leadership were deeply concerned over this, they knew that hiding or caution would not prevent other expanding empires such as the Klingons, Romulans or the Tholians.
With a little urging from Section 31 a bill was passed that started a new tradition, inspired by the first Warp 5 starship and its historic voyage into the unknown, A new Enterprise would be commissioned and despatched on a 5 year mission. famously to explore, and to boldly go.

These pathfinder vessels were manned by the best of the best, exemplars of federation ideals.
Every vessel in the fleet would be held in comparison to these ships for hundreds of years to come.
In this way, the peoples of the Federation knew who they were and they were happy.

Section 31 knew better though. There was work to be done.
Goodwill and inquisitiveness could only go so far, and to many races would simply be regarded as childish or naive.
With that, a long campaign of careful social manipulation and calculated interference was established in many cultures.

Romulans
The Romulans were a deeply distrustful society, stratified and arrogant by human standards.
The only trust was within families and the ties of loyalty were often written in blackmail or blood.
In times gone past, the Romulan civilisation had been wide-spread and deeply tribal, but a combination of a growing population and the predations of nearby interstellar species left them forced to work together.
As a people, the Romulan Star Empire had become deeply xenophobic.

Section 31's goals in the Empire were simple, to bring about a softening in the hearts of the Romulan populace to make them more open to other cultures, particularly the Federation.
They achieved this with many means, most notably the quiet discrediting of members of the Senate, supporting the activities of more moderate natured individuals, even assassinations where necessary.
The process took nearly 200 years, but by the mid 24th century, the Empire was on speaking terms with the Federation and had even allied with them against the Dominion. War was off the table.

The Dominion
The Dominion represented just the sort of threat Section 31 existed to combat.
A vast interstellar empire, expansionist and aggressive.
The Federation stood no chance in open war with such an empire.

Fortunately Section 31 encountered them early.
Extensive surveys of the Federation's neighbours revealed curious references in the Bajoran histories and even clandestine reports amongst the Cardassian Obsidian Order of a Wormhole on the edge of the Bajoran system.
Section 31 operatives scoured the system, searching for the expected signs of a Wormhole, they found it in the form of a source of Tachyon Emissions and were able to traverse it.

On the far side, they found many thriving civilisations, but most concerning of all was the mention of The Dominion.
The Dominion they found was vast, extending across much of a spiral arm of the galaxy. A credible threat to the entire Alpha Quadrant, let alone the Federation.

Something had to be done, and so a fleet was dispatched at high Transwarp.
They would cross dominion space and establish an industrial base in the path of Dominion expansion into the far end of their spiral arm.
The fleet's task was simple. Engage in total war against the Dominion in order to draw their resources to regions far away from the Bajoran Wormhole. The Dominion military would be distracted with their forces tied up in warzones elsewhere, in this way time would be bought in blood for the federation to make allies with its neighbours and gather its own military strength to defend itself against the Dominion.
The fleet itself took the role of a star-faring race with no homeworlds of its own. It publically claimed a vast tract of territory well in excess of any the Dominion could safely ignore, then rigorously defended it against all-comers.
As the Dominion's forces pushed deeper into Section 31 territory they were met with increasing resistance from vessels whose designs owed nothing to Starfleet. these vessels were entirely automated, many serving as heavily armed missiles which would explode amongst the Jem-Hadar attack ships with devastating effect.
Others were titanic dreadnoughts, comparable in size and power to Dominion Battleships.

The Western Fringe War (as it would come to be known amongst the Shadowfleet) ground on well beyond the Dominion War with the Federation, beginning in 2370 and continuing on for nearly 20 years
By 2390, nearly 15 years after the cessation of hostilities between the dominion and the federation, the Section 31 forces would reduce in number down to a few dozen vessels which could be found roaming the region until eventually the Dominion "won" the war and claimed the territory once and for all.
No Section 31 crewed vessel was ever captured by the dominion.

During the Dominion War, and in the run-up towards it. Section 31 became increasingly politically active, engaging in a number of clandestine efforts to ensure the Romulans and Klingons would enter the war to assist the Federation.
During this time an extensive recruitment drive became necessary to bolster the number of field agents.
One such prospective agent was Doctor Julian Bashir. Bashir was a perfect candidate, but for his high profile role. Ordinarily he would have been passed by, but his nature as a genetically enhanced human made him far too enticing a candidate.
Unfortunately his moral convictions prevented his use beyond a couple missions and he quickly revealed his experiences to his colleagues.
This was the first glimpse of Section 31 the Federation at large had experienced in 200 years.
It would not be the last, however it was entirely intentional.

"Director" Sloan was tasked to present the impression of a much more insidious version of Section 31. The impression intended was one of small cells, of an organisation inside Starfleet. A Secret branch of Starfleet Intelligence
The Federation would never suspect the true scale of Section 31 or the presence of its Shadowfleet operating within their borders until the Broken Mask incident ten years later.
The presentation of the Section 31 Manifesto was also intended to test the waters with the Federation, to see how truly strong its moral conviction was.
Doctor Bashir passed this test with flying colours. Starfleet Command did not.

Another notable Section 31 operation during the Dominion War was the creation of a Morphogenic Virus to poison the Founders, a tactic calling back to their first major action against the Klingons.
It was during this operation that Sloan died, committing suicide to prevent a cure for the virus being retrieved by Bashir and his colleagues.
He was unsuccessful in his efforts but the counter-virus was disseminated to the Founders in exchange for a peace-treaty which ended the war.

Broken Mask

In the year 2385, A large scale Borg strike force reached the Federation. The destruction of their Transwarp network had forced them to journey via more conventional means.
Two entire sector fleets of many hundreds of capital grade ships were destroyed, taking much of the Borg fleet with them, however four Cubes as well as a number of Spheres were able to reach Sector 001 and the Sol System.
With the Homeworld defenceless and no prospect of federation reinforcement, Section 31's fleets were ordered into the fray in what would be known later as the Broken Mask incident.

To the astonishment of the beleaguered defenders, a vast armada of ships dropped out of Transwarp almost directly on top of the Borg fleet, striking with weapons never seen in the Federation and with the full force at their disposal the Section 31 battle-force engaged the Borg, two of the cubes were destroyed within the first few minutes and when the fighting stopped some 45 minutes later, the tattered remnants of the newcomers held orbit, Debris from the battle would continue to fall upon the earth for years to come.

This marked a dramatic change in the federation and a devastating crisis of faith for both Starfleet and Section 31. In the end, Section 31 was officially denounced by the Federation. The Federation didn't want their help, they believed they didn't need it.
Section 31's fleets returned to their dark moorings and licked their wounds, they would bide their time until they were needed again.
With Section 31's existence revealed, many races in the federation and around became increasingly paranoid about what level of interference had been enacted to guide them into the fold, deep examinations of the circumstances leading up to their joining the Federation revealed many oddities and discrepancies. Secessions from the Federation were few however as the ties binding them were strong. The collective feeling was that whatever their history, they were better moving forwards together.

Starfleet initiated a purge across every level of its organisation, attempting to cleanse itself of Section 31's operatives and influence.
It was largely successful, though operatives would continue to infiltrate Starfleet as time went on.

For Section 31, life went on more or less as normal. Their forces were depleted, but easily rebuilt. the veil of secrecy might be down, but with no ability to find them, the Federation was unable to do anything further.
The Broken Mask incident was merely a setback in the grand scheme of things
The greatest problem was the damage to relations between the Federation and its neighbours. The Romulans in particular would regard it as vindication of their mistrust of the Federation. The Klingons never learned the true extent of Section 31's involvement, but relations continued to sour until a minor brush-war with the Cardassians brought them together again.

Section 31 Assets

The Shadowfleet

The Shadowfleet was the strong arm of Section 31.
Initially comprised of a few vessels, typically modified civilian craft, mid-sized freighters armed and equipped with military grade equipment. Section 31 quickly realised the need for its own vessels. They would need to be true military craft, intended to fight wars and engage in privateering actions.
The earliest Shadowfleet vessels were taken from Starfleet designs, however as Section 31 grew apart from its parent body it developed its own designs and conventions.
These new designs were explicitly intended to distance themselves aesthetically as well as technologically from Starfleet. The idea was that should a Shadowfleet vessel be observed or worse, captured, it wouldn't imply Federation involvement in whatever activity it was undertaking.

With the limited personnel at the disposal of the organisation, Shadowfleet vessels were typically heavily automated, extensive use of androids and semi-sentient automata for crew and systems repair meant that Shadowfleet vessels were often highly independent.

Taking cues from the Romulans, most Shadowfleet vessels were equipped with Cloaking Devices and in some cases, holographic emitters capable of camouflaging them as another vessel. This was used to great effect in False-Flag operations. Keeping tensions between their enemies was an easy way to keep all eyes away from the unthreatening and peaceful Federation.

When it came to direct warfare, the Shadowfleet turned to the use of automated dreadnoughts and swarms of drone craft numbering in the thousands.

The Shadowfleet contained many designs of vessel intended to fit in with Starfleet designs. In some cases the opposite was in fact true.
Classes such as the Defiant class, Sovereign and Prometheus all stemmed from Shadowfleet combat Chassis and their design-elements were presented by puppet design-teams tasked with creating ships to fight the Borg.

Cloaking Technology

The Treaty of Algernon forbade the Federation from making any use of Cloaking technology, however as Section 31 operated entirely clandestinely and with no real attachments to its parent organisation the Shadowfleet made great use of Cloaking devices throughout its history, starting with captured Klingon devices and soon manufacturing their own.

This technology remained relatively static through much of Federation history though many improvements were made in the fields of emissions masking and other stealth practices.
The biggest two breakthroughs were the development of a means to mask against Tachyon beams and the development of a Phase Cloak.

The Phase Cloak was initially prototyped under the auspices of Starfleet Intelligence. As was so frequent in such test vehicles, the crew had no idea their commanding officer Erik Pressman was a member of Section 31. They mutinied and the test craft was lost.
Some twelve years later Section 31 made use of the Enterprise to recover the lost ship and its illegal hardware before the Romulans could find it.
Pressman was court-martialled for his role in it, but the Phase Cloak prototype was retrieved by Section 31 operatives and the technology went through several more iterations before achieving relatively widespread deployment.

Phase Cloaked observation stations and so-called "Ghost Ships" served the Shadowfleet well for decades to come.
One particular tactic was the use of Phase Cloaks to intersect and board ships clandestinely. Operatives would use special arm-bands to disrupt the phase-cloak locally and step from one ship to the other.
An adaptation of this technique could be used to abduct personnel without them ever realising. A holodeck could be configured to resemble a corridor and the unsuspecting target would walk through a hole in the phase-cloak and seamlessly straight into the holodeck on the cloaked ship

Transwarp Technology
Initial Starfleet experiments with Transwarp were an abject failure, the high power of the warp fields used in Transwarp would cause Dilithium to become unstable and cause a Core Breach, Starfleet as a whole moved away from the idea of Transwarp until the appearance of the Borg and reports of USS Voyager's encounters with other Transwarp capable races.

Section 31 however continued the research, developing by the turn of the 24th century a functional and stable Transwarp drive. This drive quickly became the standard issue aboard all Shadowfleet vessels.
The unparalleled mobility this afforded imbued Section 31 with radically greater flexibility in Shadowfleet deployments.
Previously the Shadowfleet was required to spread itself across the Federation and due to communication constraints could not be easily recalled to deal with emerging threats. With the advent of Transwarp, the Shadowfleet remained largely on standby at secure deep-space bases. able to react at extremely short notice to whatever missions might arise.
This unrestricted movement began to diminish as Starfleet began actively watching for Transwarp signatures that might herald the presence of Borg Vessels. Unknown contacts began to be picked up by federation listening posts until Section 31 was able to find a way to mask their trails.

Industrial Strength

Initially, Section 31 was only able to piggy-back off of starfleet assets, its operatives infiltrated the crews of Starfleet ships and stations. Most of its Black work took place aboard privately owned and civilian craft, however these rarely had the freedom or range to reach hostile powers.
Use of captured craft quickly became the norm and Section 31 rapidly developed an expertise in alien technology.
The necessity for keeping these captured craft out of sight from Starfleet meant that the early Shadowfleet remained firmly in deep space. constructing or capturing facilities in a variety of remote locations outside of normal shipping lanes. Outside of its primary agenda, Section 31 operated as privateers and pirates, even preying upon Starfleet and human-built vessels from time to time to build up its strength and recruit new members.

As time went on, Section 31 was able to quietly co-opt Starfleet vessels, Mothballed ships would be quietly erased from computer records and reactivated as fully equipped ships once more, ships would be "lost" in remote regions only to be recovered and refitted with Section 31 hardware.

Section 31's industrial base was primarily constructed in regions passed over as too remote or hostile for the Federation. Rogue planets between star systems provided secure harbours and virtually unlimited resources and these were prized above all others.
For the construction of the Shadowfleet the organisation turned to large scale replicator technology, manufacturing entire sub-sections of their vessels wholesale and assembling them in great orbital installations.

Androids
Section 31 was ever a small organisation, at its height its numbers could be rated in mere thousands.
To make up crews and operate its industrial facilities, the organisation turned to one of its fringe-members. Doctor Noonian Soong. A brilliant Cyberneticist, he worked for Section 31 through much of his youth designing Androids of many marks. the Soong Servo-droids were limited machines, capable of following orders and enacting a multitude of standard protocols, they were short of sentience and required commands from a flesh-and-blood captain in order to operate a starship.
Physically, they were tritanium skeletons, sheathed in positronic circuitry and servos, wrapped in durable plating intended to protect them from impact damage.
The Section 31 Androids were not intended to pass as human, only to fill the roles of a human crew.
In this they excelled and many thousands of the machines were built.

Soong's work however was largely unknown in the Federation and his work frequently covered up by Section 31's operatives. This association largely ended in his old age as Soong retreated to relative obscurity on Omicron Theta, There he constructed what would be known in the Federation as the Soong-Type Androids. built upon his previous work, these were constructed to appear human and Soong's efforts from this point were largely aimed at improving their AI, something Section 31 held little interest in.

Prior to the use of Androids however was the M-5 Multitronic Unit. An effort to produce shipboard computers capable of enacting Section 31's missions independently.
The initial Testbed for this project was the Enterprise under the command of Captain Kirk and operating with only a skeleton crew.
Initially the computer performed flawlessly, however it began to operate contrary to orders and act in its own interest. Ultimately the prototype was destroyed and its designer Doctor Daystrom had a nervous breakdown.

Later however, the same technology would be used in a limited fashion to operate the Shadowfleet's drone craft and strategic computers.

Time Travel
The Federation at large has an established ban on Time Travel technologies. This rule was instituted towards the beginning of the 23rd century after a number of temporal incursions made it clear that it was too dangerous to meddle with.

Section 31 largely agrees with this policy, however a number of incidents in its history demonstrated the need for a force to deal with this.
The reports from Voyager of the Krenim time technologies, The Borg's time-travelling to stop the federation from existing and a number of other events all proved that someone needed to be looking out for such events and prepared to stop them.
Good fortune could not be relied upon.

To that end, Section 31 established a spin-off organisation known simply as Temporal Investigations.
They held the same core goals, The survival of the Federation and its ideals by any means necessary. but focused on temporal threats.
These operatives were rarely seen, but held fewer qualms about revealing themselves to those who meddled with time-travel. Their goal was to make it clear that there were rules, and people enforcing those rules.
This organisation initially made use of warp-Slingshot techniques such as those used by Kirk's Enterprise in the 22nd century, but later developed much more sophisticated techniques as well as methods of shielding themselves from the effects of changes to the time-line.
Their forecasting technologies would serve to keep the Federation on the straight and narrow path to Galactic Supremacy for centuries to come.