The body of Indiana Jones can be found in a dungeon called Omalen Ancestral Tomb. Apparently a rock fell on his leg, dooming him to a slow death. There's a scroll that records his last thoughts, signed "Indie". It also mentions that his father made jokes about his childhood pet. In the movie The Last Crusade, Indiana's father exclaims at the mention of Indiana's name: "We named the dog Indiana!" This would be the childhood pet the scroll mentions.