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?