Deck of the pirate ship take stairs to the platform above, pick the axe and once you have picked the axe descend the stairs case and press the action which is key hanging near the rope the cannon. Move to where the cannon is and press the action key again, and the Scooby will throw the cannon in the water and get the key. Using the axe that you picked, cut the string so that Scooby comes down, pick the key and open the door near the stairs. Inside the gun pile carefully sneak behind the pirate, and move to the box to the right side of the stairs case and click on the action key click the action key again, move to the stairs going down and move back to the deck by pressing the action key.
Back on the deck move to the top stairs and pick the dark pirate cloth and use it to hide Scooby's face whenever you hear the voice of the goon by pressing the action key. Pick the rope which is tied to the ship's side and tie it to the trap at the middle of the ship. When the first goon comes on top of the deception door, press action key and trap it. The second goon will be near the platform. Go near the gun powder bundle, press the action key in order to place the powder on top of the floor. Wait for the goon to come above the gun powder barrels and light it by using the torch.
The Ghost pirate once you have gone into the cabin, take the net hanging by the stairs. Using the action key, climb the rope near where you threw the cannon. Press the key specifically the action key to throw the net over the pirate ghost to trap it.