I see Section 31 as having two major roles in Coreline: A) They are attempting to push for the militarization of Starfleet, including the development and construction of ever more advanced and powerful warships (like the USS Vengeance from Into Darkness, which some non-canon material suggests was not the only Dreadnought-class vessel), and B) They are securing alliances with such groups as the Titans, that have more compatible ethics to them, with the motive of having them into do things most of Starfleet would have moral objections to doing, but require resources beyond those of Section 31 itself. In some cases they might simply hire mercenaries, but in other cases it is considered more prudent to convince others that whatever Section 31 wants done will benefit them as well.
Going back to Costa Rica for a moment, if they are supposed to be involved in manufacturing technology on behalf of Starfleet, maybe Section 31 might take an interest in the nation. After all, Costa Rica's nature as a less important nation could be an asset to Section 31. So maybe they are involved in the nations' affairs. They might seek to use Konoha specifically to help with the security of Starfleet operations in Costa Rica including, possibly unwittingly, Section 31's. On the other hand they could see Konoha as a threat and seek to drive them out, but probably without a war that would bring unwanted attention to the nation.
While the Vengeance was destroyed it is large and powerful enough that it may well be equivalent in many ways even to the dreadnoughts of the 25th Century from Star Trek Online, since the alternate universe Starfleet was able to advance more quickly through analysis of the Narada (the Romulan ship from the first new Star Trek movie) and the fact that is a a pure warship unlike many other vessels in Starfleet. It is more than twice the size of the Galaxy-class including the Galaxy x dreadnoughts, making it amongst Starfleet's largest vessels and with some additional development incorporating even more advanced technology, may be more dangerous than many larger vessels, including the Imperial-class Star Destroyer. Section 31's supporters say that such a large vessel is necessary to check the threat of the massive warships used by groups like the Imperium of Man and the Galactic Empire. While the Dreadnought-class has yet to be put into production, Section 31 has been successful in securing the production of a larger number of escorts and other heavily armed vessels than at any other point in the Federation's history, including smaller vessels like the Defiant-class and it's variants, as well as larger vessels like the Avenger-class battlecruisers, Prometheus-class advanced escorts, and the aforementioned Galaxy x-class Dreadnought even vessels as large the Typhoon-class battleship, and the Odyssey and Jupiter-class dreadnoughts (the latter is actually slightly larger than the Dreadnought-class, but isn't as advanced as some ships that are smaller). Section 31 has also been acquiring ships used by other factions for Starfleet. The Victory-class Star Destroyers and Venator-class Star Destroyers are considered outdated in the GFFA, but are actually pretty formidable compared to many ships of the Milky Way galaxy and even the Imperial-class is slowly being replaced by more advanced vessels like the Pellaeon-class and Imperious-class. The powers of the Milky Way Galaxy have been taking advantage of this to purchase these vessels for their own fleets. Starfleet has an increasingly close relationship with the Mon Calamari as well and the Mon Calamari have built a few ships for Starfleet, designed from the ground up to support a mix of Starfleet and GFFA technologies. Section 31 is also pushing for Starfleet to take as much advantage as they can out of their alliance with the Romulan Republic (from Star Trek Online).
Many of those I noted as allies of the Titans would be allied with Section 31 as well. The United Earth Directorate and United Federation of Planets have many differences, especially in there attitudes towards aliens, but they also have many potential mutual enemies. Thus Section 31 works with the UED against these enemies, providing them intelligence and data that in order that they might take action when Starfleet is unable or unwilling. Section 31 works with the Titans with certain situations involving the Earth, including fighting organizations like the AEUG which could threaten Section 31's interests as well. Section 31 has secretly arranged for Starfleet personnel to support the bio-weapons projects of the Galactic Federation, even supplying Federation technologies that would be useful for their efforts. Samus Aran has attempted to track down a specific ship under Section 31's jurisdiction- the USS Soong, a Miranda-class vessel with a genetics research module, yet she has been unable to, since, for one thing it does not officially exist and thus there are no records of it in Federation databases and also it spends most of it's time on the move outside of Federation space. She believes that Section 31 is allowing the Galactic Federation to use it for it's purposes. Section 31 has been in communication with Thrawn, who has offered the Federation to join his Empire of the Hand. However, it will be a considerable amount of time before any such negotiations come to fruition, since despite the Empire of the Hand not being quite the same as the original Empire that is obviously quite incompatible with the Federation's values, and the fact that Thrawn generally allows local goverments to maintain their original forms, the Empire of the Hand still isn't quite fully compatible with the Federation itself.
