We already know how John dies.
D: I've made a great discovery!! Despite being in a test... I managed to reread One Piece Volumes 1-48!! And my discovery was... In "The Highest Authority in the World", Chapter 233 of Volume 25, Buggy and his crew are searching for Captain John's treasure in a cave. And then in "Perona's Wonder Garden", Chapter 451 of Volume 47, there's Captain John again! Is this a super-huge discovery, or what?! Who IS Captain John? Just how cruel was he? Tell us, Ei-chaan!! P.S. Tosa Danji
O: Yes, you've found it. Well spotted. The man whose treasure Buggy and crew were searching for had become a zombie at Thriller Bark. Look close at Captain John's stomach. He has several slashes in his belly, and two swords sticking right out. These were the marks left when his crew killed him for keeping the treasure a secret from them. John died, and the location of the treasure became a legend, lost forever.