You may have noticed that we talk a lot about conspiracies around here. There are a couple of reasons for that, the primary and most important being that they are interesting. Really interesting. Looking at the world through a conspiratorial lens is simultaneously empowering ("I'm important enough that they're trying to get me!") and disempowering ("Their resources are so vast that there's no way that I can truly oppose them!"), but the real power of the conspiratorial worldview is that it removes a great deal of randomness from the world. If you can tie events both great and terrible to the actions of a powerful secretive cabal, all the terrible entropy in the world may still be terrible, but it at least starts to make a dark kind of sense. And let me tell you, the real world rarely makes sense. But your game doesn't have to take place in the real world, or even a proximate simulation thereof. So why not put a little bit more depth into those shadows? You'll be glad you did.

If You Build It...

At its core, every conspiracy is about acquiring and exercising power and control. Conspiracies acquire both using collusion, coercion -- and most of all secrecy -- to subvert, bypass, or eliminate opposition or obstacles. I suspect most games that include them will be about preventing the conspiracy -- regardless of its nature -- from doing just that, but in rarer cases you might decide to build a game around the idea that your PCs are the conspirators themselves -- think Asimov's Second Foundation vs. the X-Files.  Although all conspiracies are different (unless, of course, you subscribe to the theory that they are all merely the outward faces of a single master-cabal), they must have some key elements to be viable:

Puppetmaster(s)

Though a conspiracy may have a single originator — a master puppeteer pulling all the strings — it must by definition include other conspirators, who themselves may employ other witting or unwitting subordinates in the service of the cabal’s goals. The upper echelons of the conspiracy will be at least tacitly aware of its true intentions; the lower echelons almost certainly will not. The Real Truth will always be found at the center of the web. In your game it might be wizards (or The Wizard). Or Reptoids. Or the Council on Foreign Relations.

Secret Aims

The conspiracy wants something, and it’s not something it can get easily or openly. The goal may be as simple as the acquisition of personal power, or as complex as the engineering of a specific future event. Ruling the world seems like a popular choice, as is, ironically, ridding it of human life. The end for which a conspiracy strives need not be strictly evil, or even entirely contrary to your PCs' goals. (It usually helps, though.) Regardless, there’s always something that drives a conspiracy into the shadows. After all, if the cabal’s intentions and actions were truly noble and its actions acceptable, it could operate in the open. Unless it's being run by the Reptoids.

Compartmentalization

Even when dealing with willing co-conspirators, successful conspiracies strictly compartment knowledge of their activities and intentions to ensure that they are not discovered until or unless they have acquired enough power to ensure that secrecy is no longer necessary. This compartmentalization prevents unwitting slip-ups or opposition discoveries from endangering the entire operation: you cannot spill a secret you do not know. As with so many things, this is on a need-to-know basis. The PCs don't need to know; as the game progresses, it may become more about what the conspiracy needs them NOT to know.

Power (But Not Too Much)

Although your conspiracy must have at least a modicum of power to be effective, it must lack the necessary leverage to completely overcome those who would oppose its ends (or the means it employs to achieve them). After all, if it had THAT much power, it wouldn't need to operate from the margins. This is why conspiracies often use threats, blackmail, or assassination to secure cooperation from those who would oppose them (or to replace their enemies with more pliable individuals) – they may have enough power to nudge an individual, organization, or even an entire military industrial complex to follow its desired path, but not enough to force the issue in an open conflict.

Plausible Deniability

Even when secrecy fails to protect the conspiracy from undue scrutiny, deniability — the conspiracy’s ability to sow doubt as to its intentions or even existence — can prevent any serious backlash against the core cabal, even if specific members or activities are discovered. Consequently, conspiracies are most likely to flourish undiscovered in large organizations with complex bureaucracies, which give them ample opportunity to hide their activities from unwanted attention, or at worst use internal organizational boundaries obfuscate the true purpose of their actions from others who do not share their goals. PCs who begin to make progress combating the conspiracy’s machinations may find key suspects or allies suddenly moved to new jobs or tasks out of easy reach, or even find that treasured sources die mysteriously when the PCs start to move against whatever part of the conspiracy they have revealed.

Now, if you'll excuse me, I've just learned that I've been reassigned to an isolated military base above the Arctic Circle.

...wait a second...