Complex sentence: Although happy to see his former captain, Bootstrap reveals that Davy Jones sent him to remind Jack of his debt due to him, having raised the Pearl and given thirteen years as its captain, and then become another crewmate aboard the Dutchman.
Split into simpler sentences: Although happy to see his former captain, Bootstrap reveals that Davy Jones sent him to remind Jack of his debt due to him. Jones had raised the Pearl and given Sparrow command for thirteen years as its captain in exchange for Sparrow becoming a crewmate aboard the Dutchman.