After taking over the control, shoot the enemies who attacked the ship. Cross the boat's deck and turn right, where you'll encounter several opponents hidden behind wooden chests. Eliminate them, pick up two bottles from the shelf and go east. You'll run into the bandit which is holding the hostage , so I recommend using slow motion and firing one, precise shot at the enemy's head. Turn left and kill some more gunmen. Now, move the wooden bar .
Go west and take advantage of the cannon located on the left side. Destroy all enemies' boats . After the fight, move in west's direction and clear the whole lower deck from the opponents. Go up the wooden stairs, run up to Ned defending himself, and help him in fighting with some evil gunmen .