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So far I understand that the Synod is extremely zealous and jealous of the College of Winterhold, I also know that they were after Oculory of Mzulft for unknown reasons (maybe for the Staff of Magnus?). With the College of Whispers, I know that they helped defend Imperial City when Umbriel came about, and they also get help from and summon daedra, does anybody else know where I can get more information about the two derivative Mages' Guilds of the Fourth Era, or if anyone knows a lot about them, please tell me.

The only information about either of them asides from Skyrim is the two Keyes novels. The information we're given on them is very scant. There's less than a page total about both organizations from both books, the way I read them. They're very political, and often competitive with one another. That's really most of what's known. They can cast Levitation spells, like the old ones from Morrowind, and have invented several new potions and spell types, but as I said other than that we know literally nothing.

edit: There's a lecture about them in the College of Winterhold in Skyrim:

Faralda's Lecture: The Synod and the College of Whispers are investigating the College of Winterhold. Faralda remarks the College of Whispers prefers magic banned by the Synod, like Necromancy and Conjuration. The Synod wish to find supporters, and the College of Whispers wish to discover darker magical practices so they can prove the Synod are a political minority. The College of Winterhold remains neutral on the matter. She tells students that if they are contacted by a member of one of these two organisations, they should say nothing and merely refer them to the Master Wizard.