"man Henry was talking about when he ws being held in the armory was him or is there still a brilliant mastermind running the show from somewhere on the island. Maybe Jacob?"

This is the closest to the truth I think. Jake Alex's boyfriend doesn't nessecarily mean Jacob, I think Jacob could well be the brilliant man in charge of everything. Kinda unlikely that this is the eye patch guy because I think he's just another poor sucker stuck in a hatch.