Antagonistic Organizations
"Actually, those guys are just bastards. We fight them."
What makes an antagonist organization different from a "normal" organization in After Sundown is not that they are "the bad guys" - after all it is abundantly clear that a substantial number of people in all the supernatural societies are bad guys. These organizations are filled with blood drinking monsters. No, the salient thing about the Antagonists in this setting is that they are not willing to live and let live with the members of other Syndicates and cults. So while it is entirely possible to have a story in which one character is from the Makhzen and another is from the Communes, it is basically impossible to have a cogent story in which one character is in the Marduk Society and the other characters are not.
The assumption then is that the antagonist organizations will be NPC only. The player characters will be members of the standard Syndicates or independents and as such the warriors of the Shattered Empire who show up at all it will do so as enemies. It is entirely possible to play a campaign in which every character is a member of the Marduk society, and that's fine. If you weren't OK with playing a game that skated closely to the edge of evil you wouldn't be playing a game about vampires and werewolves.
However, it's equally important to note that just because the King with Three Shadows may be a villain who is basically at war with the World Crime League, that does not mean that anyone is automatically on kill-on-sight terms with anyone else. Even these antagonistic organizations have diplomatic ties of some sort or another with all of the major Syndicates. These ties are strained, and ambassadors are sometimes recalled, but actual shooting wars have causes, beginnings, and negotiated ends.
The Marduk Society
"We've slain the monsters of the world until they skulk in darkness like rats. Did you really think the darkness would protect you?"
In ages past the mighty sky wizard Marduk fought with the great Tiamat and slew her, saving humanity from her dark tyranny. As the savior of humanity, Marduk became a wise and just king who ruled over Sumeria thousands of years ago. He passed his magic down to disciples, and in classic fashion they perverted everything Marduk stood for and are now a terrifying edifice.
The Marduk Society retains the ancient magics of Marduk himself and continue to hunt supernaturals, nominally to save humanity from the oppression of supernatural influences. However, the leadership of the Marduk Society actually are supernatural creatures. After ruthlessly hunting down the spawn of Tiamat for generations they found that they were able to grant themselves immortality by eating the flesh of Leviathans, a practice which in reality transforms their elite membership into Leviathans. The sorceries left behind by Marduk are in truth no different from the sorceries of any Witch, and thus it is that the core membership of the Marduk Society are no different from other supernaturals save for the hat they wear and their intense desire to not get along.
Marduk's magic draws heavily upon human fear and suffering to use as power. However, while the historical Marduk apparently used this as justification to wander the lands righting wrongs and saving the endangered, the modern incarnation conspires to make mortal governments oppressive and ruin the lives of children. Ideally they claim that once their war is won they will make all human society utopic, but there is no particular reason to believe this is true.
Sample Encounter: A black van pulls up and six men in black suits get out. They are reasonably professional, have tranq guns and heavy pistols and strongly suggest that the protagonists get into the van. A couple of them are even mutants, and it's probably best to not think about how they got that way.
The King with Three Shadows
"How nice of you to join us. You can share the same fate they are going to suffer."
Long ago a powerful mortal king married a queen of the fairies. Abandoning his kingdom of men to wither and die, he took a new name and attained everlasting life with a grim bargain with Demons. A bargain that ultimately hurled his kingdom into the deepest pits of the Dark Reflection. The King with Three Shadows has become as the fairy are, and he lives forever without changing. He is now their dark king, and commands the mirror goblins - an army of fairies and demons which do his dark bidding. He is supported in his endeavors by three powerful Fairies - The Three Shadows of the King.
Fairies and Demons have a difficult time getting to the world of man at all, and must pass through a reflective surface to do so. More powerful fairies and demons need more specific mirrors through which to pass, and thus usually require that these doorways be custom built to draw them through. While a minor mirror goblin might be able to come through a pool of water or a pane of glass, powerful demons need a mirrored surface of exacting specifications - for example one might require a mirror at least 2 meters across made of bronze and polished with olive oil, lemon juice, and human blood.
The King with Three Shadows himself requires a titanic and exacting mirror to again trod upon the Earth, and it is thus that he is forced to send minions through the portals to acquire the strange materials and specific events they need to allow him to march across the threshold with his demonic army to conquer the human world.
Sample Encounter: Four mirror goblins are running down the sidewalk of the broad suburban street with an empty sack. As they pass, the streetlights flicker and dim, keeping them in the shadows. If the protagonists follow them, they see the gibbering villains break into a nondescript house and come out again with a struggling sack about the size of a young child. They then clamber back down the street and meep their way into a different house. If still unmolested, they make their way to the bathroom mirror and make good their escape.
The Shattered Empire
"They have learned nothing, and they have forgotten nothing."
According to the Shattered Empire there was once a mighty nation which ruled over all of humanity with magician kings. Where this kingdom actually was, when it existed, who the people were who ran it, and what the cultural traits of it were like are all lost to time. The Shattered Empire calls itself a dozen names: Ur, Atlantis, and Golgatha to name just a few. And while their stories of their glorious days of world ownership are somewhat conflictory, and quite possibly exaggerations or just plain lies, they are nonetheless willing to kill people over their world conquest plans. And that makes them dangerous.
The very top of the Empire is called either the Rain King, the Masked Prophet, or the Once and Future Emperor. Whether these are three different people having a power struggle or one man with a variety of titles is not clear. Cells of the Shattered Empire hide in cave systems, deep in jungles, and on top of forbidding mountains. They collect powerful magics and threaten the world with them.
The primary bones of contention between the Shattered Empire and the other Syndicates have to do with rulership. The Empire holds not only that they should rule all the other supernatural creatures like in the old days, but that they should rule all of the humans like in the old days too. And yes, that really does mean like the old days. Many of the members of the Empire believe that allowing humans to work bronze was a mistake and that such mistakes should be corrected.
Sample Encounter: The meeting is going well enough when it is announced that a messenger has arrived. A confident and wild-eyed Troglodyte strides into the room dressed in a coarse toga and trailed by some mad looking ghosts. He points his claws accusingly at the city officials and makes the pronouncement that The Empire has uncovered "the great bell" and you all have a fortnight to surrender the city. Then he and the ghosts fade into The Gloom.