There are a total of 10 Naval Forts, one of which is already captured in the main story memories. In order to take over a fort you must first destroy all of its defenses (3-9) and then dock and defeat the fort's Captains (2-3). Once the Captains are defeated you can enter the war room and kill the fort's Commander to free the fort.
Captured forts will then be under your control and attack British and Spanish ships that pass by.


