Council of Shadows

The Council of Shadows is one of the many mysteries of the Grand Empire. It was destroyed multiple times during the recent imperial history, yet somewhat it always returns. The Council of Shadows is the Grand Empire-wide criminal syndicate (that often ends up having significant influence among the criminals in the neighbouring countries) that somehow keeps existing, no matter how many times it is annihilated. That alone is... suspicious.
It is a long-term imperial suspicion that there is some greater power behind the Council of Shadows - yet no matter how much time passes and how many arrests are made, nothing is found. A really tricky Ancient? A surviving (or shattered) Old God? Proditio, the Hierarch of Dice, the only fallen high god without openly stated allegiance to any faction? A carnivorous plant from space that is somehow acutely interested in human vices? Any of the states explanations has equally expansive evidence to support itself.
Whatever it is, the Council continues to exist, with the Grand Empire having a bit of a mixed feelings towards it. Sure, it has commited numerous atrocities during the past five centuries of operations. Sure, it regularly breaks the imperial law and does things that the Grand Empire really dislike in general. However, it's also acutely aware that without the Grand Empire, it simply cannot live on - and so it's quite common for the local groups of the Council to at least try to act against the incursions from the Lost Lands, isn't entirely adverse to making some under-the-table deals concerning what it can and what it can't do, and is often useful to do things that the Empire itself can't - or shouldn't - do. Such as occasional secret assasination of a troublesome political opponent. It also, more often than not, ends up being the only stable authority in various slums, which means it's also able to keep them from being too much of a problem.
The Grand Empire knows that whatever it does, it simply doesn't have the power and ability to free itself from organized crime, and the Council plays an important role in preventing the regular wars between groups of said organized crime. To a degree, it is tolerated. However when the current iteration of the Council goes a few steps too far and infuriates the Empire, the hammer falls and the entire organization is decimated almost into extinction. This is a Damocles sword that keeps the Council of Shadows' tame and calm. For a time.

Structure

There is always the Council of Shadows itself, a gathering of a varied number of representatives of all significant criminal organizations within the Grand Empire. Even if you do not have a Shadow of your own, they will still expect you to pay your share of 'taxes' and follow the Council's orders (and will get downright mean when you don't) for as long as your are a criminal organization within the Grand Empire, so majority of such groups end up striving to set up their own Shadow, if only to get a saying.
There were many cases of the Grand Empire managing to track down the Council itself and eliminate it its entirety, or at least majority. However the problem is that Council isn't populated entirely by heads of the criminal organizations, as many of them are voting through proxies. There were always enough groups that survived (and the Empire simply doesn't have enough resources for a total crack-down) the purges to reorganize the Council of Shadows, as the prime service it offers - namely, organizing the criminal organizations to avoid fights between crime bosses tearing the empire apart in the worst time while also moderating the criminal underworld when the Grand Empire makes an under-the-table offer - are the only thing that keeps it a viable partner to the government. And prevents it from instituting a more day-to-day crackdowns. This together with the suspected supernatural inspiration soon makes the Council of Shadows reform. With the new Council learning the lesson from the deaths of their predecessors at least for a time being.
Beneath the level of the Council are numerous criminal organizations. Thieves guilds. Assassin guilds. Underground slave markets. Drug cartels. Various small groups of mages or alchemists doing stuff that the Imperial Magic Guild and the Imperial Ministry of Production wouldn't like. Black markets. Smuggler rings. Sometimes small brigand armies in the Lost Lands, ready to plunder and pillage the less-fortunate provinces (or go for the Fallen). Each has its own organizational structures and - in many cases - is temporary. The cycle of partial destructions but eventual rejoinment of the greater organization isn't unique to the Council itself.

Military

Fighting is, generally, bad for business. It makes you lose your members, might alert authorities and so on. As a result, the Council will typically not go out to wage war against anyone, at least in the Grand Empire. It will defend its instalations - both those in the Grand Empire and in the Lost Lands - with a varied mix of outlaws, hired martial artists of less-moral schools, magicians and outcast mage, and so on. Sometimes they will even resort to hiring regular mercenaries.
This is generally enough to resist occasional adventurer or other random visit. It is not enough to resist the Grand Empire of Karadia, but in all honesty, there is just no way for an organization of criminals to gather enough power to resist it - and even if they did, it would most likely flee on-sight because fighting Empire is dangerous and the criminals always prefer to pounce on those weaker than them.