There is one thing that you don't think when you created Starfleet Intelligence, according to Memory Alpha, the Section 31 is responsible for the security of the Federation but also capable of sabotage since we know that it has created a virus that was then injected into Odo's body to destroy the Founders.
The non-canonical novels published by Pocket Books posit that Section 31 was involved in the theft of the Romulan cloaking device by the USS Enterprise (TOS: "The Enterprise Incident"), the development of the Omega molecule and the subsequent destruction of subspace in the Lantaru Sector (VOY: "The Omega Directive"), and spying upon Federation civilian attorney Samuel T. Cogley (TOS: "Court Martial"). Starfleet Admiral Lance Cartwright was established to be a Section 31 agent in the novel Section 31: Cloak, suggesting the possibility that the Khitomer conspiracy was, from the Federation end, a Section 31 operation.

In Starfleet Intelligence, I would see good adding 10 % of sabotage and espionage. What do you think? (In the original version of BOTF, Section 31 was mentioned in their DCER's editor but never used by MICROPOSE)

Section 31 was an unofficial branch within the Starfleet Intelligence and it was not controlled by them. Therefore, it would be more interesting if it was a random event, eg Section 31 murdering some Romulan/Klingon/Cardssian etc high official or stealing some tech or something similar.

Section 31 had no headquarters, no funding, and no resources, so it wouldn't be realistic or canon to give them a "building" as such in the game. Espionage and sabotage - although not necessarily internal security - are also supposed to be the Federation's greatest weakness; giving them a specific bonus in this area would therefore fundamentally alter the balance of playing the game.

The Captain might have something with having them in as a random event though. Rogue agents could certainly be an interesting one, especially if you were given the option of helping them or specifying a specific target, but the actual outcome was random; afterall, providing resources for the rogue agents would increase the chance of success, but could also increase the size of the penalty should the activity fail, since those resources could be traceable back to your empire. Conversely you could even be asked to spend resources to prevent their rogue activities - players could be given the option. If you decided to cut the rogue agents lose and work against them, the rogue agents might decide to attack you instead, but the potential damage to your relations with other empires would be removed if the rogue agents succeeded. Of course, if they went after you and succeeded, you could suffer problems with internal security or morale as the people lose faith in your abilities, or a key building could be destroyed in a terrorist attack. There's a huge list of potential consequences we could include.
It's definitely worth considering...

Hi guys (been awhile)

Why not make Section 31 some sort of hybrid between a random event and an organization in place to help the Federation? In DS9 and Enterprise, Section 31 occasionally sought out Star Fleet Officers to go on missions critical to the security of the Federation (or Earth). While the mission had an obvious benefit to the safty of humans, it typically also had very negative side effects for others (For example, near genocide of the Founders helped to bring about the end of the war but made others feel negative about the Federtion Council because they didn't give out the cure).

An example of play in the game would be for Section 31 to ask you to move a ship into enemy territory because of some kind of threat (They don't give you a reason upfront - but maybe the Cardassians are massing a fleet in a sector near your territorty that you cannot scan for some reason). If you don't move your ship into enemy territory to investigate, obviously you leave yourself open to invasion. If you do, then the Cardassians claim an "intergalatic incident" because you trespassed in their territory. However they don't invade because the element of surprise is no longer on their side.

Another example could be that Section 31 tells you to dedicate 20% more resources to Intel for the next 2 rounds. If you do, a Romulan Senator who is anti-Federation is assassinated (The senator would have become Preator in the next turn which would have caused relations to suffer. However, because the Romulans get nervous, they build 10 more Warbirds for security).

To keep game play fair, this can be expanded for all playable races

Dominion: Can do pull this off as a Founder in the field making the suggestion.
Cardassian: Can pull this off as a rogue element of the Obsidian Order (maybe as Enabrin Tain or Elim Garak)
Romulan: Rogue element of the Talshiar
Klingon: Are way too blunt in their aggressiveness to have this option. If necessary, I'd pitch this as a member of the Durass House making the suggestion (since they seem to associate with other rogue elements in Trek anyway...)

Any toughts?

nice idea , I had thought previously that we might look to include something akin to what is done in the total war series, where you get missions for you to complete from the government or some organisation.

However someone has to code it which is always the problem still something to look into later perhaps.

Regards Wolfe