The game will be taking place in Karrnath. Each character will have a connection/relationship with one of the Dragonmarked Houses, the Twelve, the Aurum or a similar organization. How familiar are you all with Eberron?
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Factions
The Library of Korranberg - "Located in Zilargo's southeastern most port city, the Library of Korranberg is the greatest repository of general knowledge in Khorvaire. In addition to serving as a resource for scholars and explorers, the library often funds expeditions to study ancient cultures or unexplored lands."
The Church of the Silver Flame - Though it's a relatively young religion, its members have battled the darkness for hundreds of years. The church hails from Flamekeep where the Silver Flame is kept. This organization is Lawful Good and seeks to purify the entire world.
The Gatekeepers - A druid sect dedicated to protecting nature from the unnatural. They spend their lives fighting aberrations and guarding against extraplanar invasion and the release of ancient evils.
The Twelve - An arcane institution funded by the dragonmarked houses, they operate out of a floating keep located in Korth in Karrnath. It is an institute for the application of magic, studying dragonmarks and more normal magics.
The Order of the Emerald Claw - The Order is a military organization that works to preserve the superiority of Karrnath. The organization was recently outlawed and officially disbanded, but its members are fanatics who work to see their vision of Karrnath come to light, whether their countrymen want it or not.
Those are the big 5 factions that will play in this adventure. If you are familiar with Eberron, you know there are tons of other factions and organizations present. You may have ties to an unlisted faction, but most everyone should have ties to one of these five.