These are multi-part puzzles. You must complete one section to unlock the next, though you can skip individual parts if needed.
If you prefer visual guides, YourGibs Gaming and AdventureGameFan8 offer comprehensive video playlists covering the full game and bonus content. Mystery.Case.Files.Black.Crown.CE.rar
To defeat Captain Crown, you must collect 13 needles from mutineers and pierce a voodoo doll to weaken him. These are multi-part puzzles
Use the map for fast travel between locations. Mystery.Case.Files.Black.Crown.CE.rar