The obvious place to start out is to detail the organisation that the PCs belong to, but if they're devoting most of their time to one of the other groups it might be worthwhile to flesh them out first. Either way, it's time to dive deeper in.
Start by deciding the components of the group. Were I to take the UN in my Deus Ex setting, we've got the following parts:
- UN Security Council
- Clan Elfpants
The UN Security Council is notionally made up of representatives from five core countries and ten rotating member states. In reality, the ten rotating states rarely vote against the five, and even if they did they could only ever force a re-vote on the issue. The Security Council is a shadowy old-boys club who like to think that they and they alone are the ones who have to stop the world falling to anarchy and lawlessness. They have full legal control over the UN peacekeepers, and the directors of both UNATCO and the UNSCIT report directly to them.
UNSCIT are the heavy-hitters, mostly made up of cyborgs who can't pass for human any more along with some nanaugs and human agents specialised in urban combat. They have enough firepower to level a medium-size city in the time it would take the rest of the world to react. Technically they are under the control of the UN Security Council, but the director is a sham and a pawn of Clan Elfpants. To all intents and purposes Chessman is in direct control, though he does bow to the Clan so they don't realise just how little hold they really have.
UNATCO are the CIA to the UNSCIT's marines. They undertake undercover missions and surgical strikes that can destabilise governments with only a few well-placed words and one building left devoid of life. The Director reports to the UN Security Council, but is given a free reign to act first and report later in situations that require immediate intervention. The Director is also deep in the pocket of Clan Elfpants, which certainly helps.
Chessman is the single most dangerous man on the planet. In addition to being a cyborg, he's very dangerously insane and has direct command over the most powerful force of augmented humans on the planet. He's aiming to turn Clan Elfpants> against itself when it starts to really bother him, but for now he's concentrating on outside threats. He has a few agents in UNATCO, hoping to increase his power base that way, but he's not had too much luck yet.
Peacekeepers are the UN military detachment. They're the Security Council's pet army, and most of them don't complain. UNATCO has compromised their chain of command rather thoroughly, but they don't do anything with that unless they have a very good reason. The peacekeepers in general are what most people think of when they think of the Security Council these days, and as such are the public face of the UN.
Clan Elfpants is not the shadowy group's real name. It's one of these big conspiracies who have their fingers in a lot of pies and are probably behind more than one group. More detail on them and their agenda when I release more of the big secrets.
Already we have a weird network. when we work out where the outside connections join it becomes more fun.
US Government agencies have infiltrated the command chain of the Peacekeepers as well as UNATCO have, and are spying on the Security Council. For their part, UNATCO have sleeper agents placed in the alphabet soup, reporting back and disrupting the chain of communication. The US don't like the UN operating on their soil, and the UN don't like the US insistence on going their own way. This hasn't yet flashed up into actual fighting, but unless the Security Council and the US government come to an accord it's only a matter of time.
The Peacekeepers are fighting a losing battle against the Thule Society. Every time they move in to clear out a nest of these multinational neo-Nazis, the Thule have been prepared and a number of soldiers have died. This isn't really surprising, Clan Elfpants is feeding the Thule just enough information that it doesn't realise the UN know of their existence as an organised group while ensuring that the serious cells are exterminated with all prejudice.
The Vatican have it easy. The UN doesn't believe that a church can be a big player in shadow politics, and that has left them wide open. Two of the Security Council rotating seats are currently held by Vatican members who are influencing the core members bit by bit. The Templars are trying their best to break in to the communications systems of the UNSCIT to find out where the bodies are hidden, but haven't yet had any success.
The NSF are worldwide anarchists, fighting for the belief that every man should be free (or at least free to be a good man). The UN, especially backed by Clan Elfpants, are the ultimate central world government. UNSCIT and Peacekeepers have both adopted a shoot first policy, and the NSF cells respond in kind. UNATCO agents have gone undercover, but a surprising number have been turned to the NSF cause. So far the two groups are close to a state of all-out war akin to the UN - Thule conflict (but without the benefit of the Clan engineering everything behind the scenes).
All that just from breaking down one node. Do that to all five: Give them subgroups, give the sub-groups relationships -- even if it's just that they don't have a relationship with anyone else. Then work out how each of the incoming lines from the pentagram mesh into each of your subgroups. Soon enough you'll find yourself with a random graph, and you'll have a real network of conspiracy.