This one apart from my previous theory on Jolly Roger being the Cap'n would be an amazing twist if we get James Hook from that Robin Williams film, "Hook", to actually be the leader of the Dark Brethren Court.
Why I think it's him.
James Hook may have drank the same chalice that cursed Flameheart Jr. and made him a Skeleton Lord, which explains why he hates them, even though he's one of them, because he cannot die, and was denied true death, if he were defeated, he'd just come back. Which to him, isn't exactly thrilling. And so he is trapped in a land where pirates die and live again.
Hook has Davy Jone's Heart?
Instead of Cutler Beckett, Davy Jones now serves Captain Hook and does his bidding, even though he is imprisoned by the Ferryman, he technically isn't dead since the heart was not in the Dead Man's Chest. Meaning, Hook still has plans for Jones along with the other members of the court.
Hook wants an Ultimate War? Trapped in the Sea of the Damned?
Like Davy Jones said in the final chapter, "We are at war!" it could mean that once James Hook sees the veil between the Sea of the Damned and the Land of the Living is broken, he will sail with all haste, like it says in the letter to Jones, possibly with an army of the Dark Brethren at his command to attack both the Pirate Lord, and Flameheart with his son! This could be an all out war Tall Tale.