You can see how it might be difficult to summarize all this.
The Winchwell and Blaenville threads all deal with a plot to kill Archbishop Tameric of the Church of Zilchus and get a local man (Father Silas Taro) put in his place.
A group of wealthy citizens with lots of underhanded dealings has been receiving aid from a harvester devil named Matukal. Father Taro has made a pack with this same devil.
Matukal works for Mammon, who wishes to promote the Crooked Stile here in Fairhaven... though he will later turn on them.
Mammon believes that desperation will drive more souls to him. He intends to bring the Fellowship to power in order to instigate a war between the Brotherhood and the Fellowship.
Mammon is actually secretly behind the series of events that led to the destruction of the Brotherhood here in the first place, although the high level paladin who led the strike force would be horrified to discover this!
The Winter Wolf in the docks thread was being shipped to a rival of Momma Toki's. This same rival is connected to the Brotherhood.
Chastity Neverton was spying on the admiral of the fleet currently docked at Fairhaven and patroling its waters. He is a high ranking member of the Brotherhood.
She had a slight indiscretion... which angered the admiral, and resulted in him contacting Momma's rival (don't recall his name offhand) to sic some nasty magebred wolves after her... if you get to the thread with the wolf combat at Momma's, that's what that is all about.
Wow, there's the whole curse of the Nordengeist family, which is related to the thread you came into. The John Doe there is actually one of the family members. That plot line is not currently being pursued... well, it is, but it's complicated...
The Nordengeist family curse is related to the beast that dwells under the city, which ties in with the shaman bag/ K'tallah spore plot.
The former head of the Nordengeist family was a member of the Brotherhood, who have made Infernal pacts with the enemies of Mammon... these pacts were made before Mammon's ambitions and enmities were realized. It was Mammon who made the move of approaching the enemies of his enemies, even though he's only seeking to set them up for a fall...
The beast beneath the city also ties in the the Praetor Syndicate thread. The Praetor Syndicate is a group of assassins, mostly nonhuman, a subsection of whom are a group of Cult of Thoon Mindflayers.
The Praetor Syndicate has one known representative in the group that Father Taro and Bax are involved with (the group in Blaenville, who are considering naming themselves the Underhaven Society... but they don't agree on much). He is a Rakshasa.
The group from Blaenville (including Meridin Caraster, a wealthy merchant) in league with Matukal are concerned that their Praetor Syndicate contingent will assassinate Archbishop Tameric, then use their willingness and ability to 'get the job done' to further their position in the group. They are jockeying to be the next big thing in organized crime. Due to favors Matukal has done for them, they have to at least pay lip service to his desire to see the Fellowship rise in power, but they secretly desire to take the place over themselves.
There's a lot more, and I know this isn't terribly organized, but this is the quick version.
Feel free to ask questions.