To have one entity that controls all three(+) factions, they must have a goal that is not depending on the success or failure of any faction – it will most likely depend on the fact that there are multiple factions opposing each other. Who is gaining anything from chaos and discord? There are several candidates present in the book:

1. Captain Xendros. She is essentially a foreign agent that cares only about fish for her country, and magic items.
2. Keledek. Just like Xendros, he uses the smugglers to get access to magic items, but he gains security by having a strong-ish government that protects his property.
3. Granny Nightshade. The more inner struggles Saltmarsh and Keoland have, the less they will bother her. The Brotherhood can be a good tool for her to keep the power of the others in check.
4. The Sea Princes. Although the loyalists hate them, supporting this fraction will keep the smuggling operations more profitable, and the princes may also get insight in possible Keoland secret plans through the loyalists. The Brotherhood gives the princes a tool to kill their adversaries in all of Keoland.

Another option that I have thought about is Xolec. Maybe he is connected to other vampires like Strahd? Then there may be Vistani involved as messengers?

Here’s my thoughts from when I ran GoSM:

Ghosts isn’t really a campaign. It’s a really un-connected series of individual mini-dungeon crawls. In particular, if you were hoping for a focus to be on the three factions within Saltmarsh itself, I will warn you that almost none of the modules have anything to do with that. The leadership divisions in Saltmarsh are just kind of there to help DMs build on their own homebrew stuff. Despite much being made of the Sea Princes, they’re more or less unmentioned in the rest of the campaign, as are the other two factions.

Notably, the modules’ antagonists break down into two major categories:

• Underwater creatures (Sahuagin in ‘The Final Enemy’, S’gothgah the Aboleth in ‘The Styes’, and a giant octopus that’s more of an environmental hazard in ‘Salvage Operation’).
• Undead (Isle of the Abbey, Tammeraut’s Fate).
• There’s also some unconnected pirates in Danger at Dunwater and a random priest of Lolth in Salvage Operation. The mini-encounters (Cove Reef, Wreck of the Marshal, Warthalkeel) are kind of just there. You might notice there’s no real theme here. Like I said, this is very open to homebrewing.

In my case, I decided I liked undead as a final antagonist better than an Aboleth. The entire thing became a plot by Orcus - my ultimate BBEG - to drown and slaughter everything in the Saltmarsh region. Everyone else - Syrgaul Tammeraut, the Aboleth S’gothgah, the Sahuagin - were either intentionally or unintentionally working towards Orcus’ goals, some being duped into doing so. This required some reskinning - the generic evil cult in ‘Isle of the Abbey’ and the Lolth priest in ‘Salvage Operation’ became Orcus worshippers.

In your case, if you want to focus on the three factions of Saltmarsh, I think you could go two ways:

• Have reach of the modules be a task or threat created by each faction. For instance, maybe the Loyalists send you on the Salvage Operation, hoping to get some dirt on Anders Solmor’s mysterious missing parents. Maybe the Sea Princes are stirring up the Sahuagin to attack Saltmarsh to break the King’s control, etc.
• Have one BBEG running all three factions. In this case, again, I would encourage you to look to either S’gothgah the Aboleth, or whoever Syrgaul Tammeraut’s magical patron is. Perhaps they are simply playing all three groups against each other to leave Saltmarsh depleted and ruined, at which point they will move in.

In either case, the political side of Saltmarsh is relatively undeveloped, giving you lots of room to work in, but also lots of work to do if that’s what you want.