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I don’t know why we are spoiling a 2 decade old manga (yes, it literally ended in 2003). Jotaro did die. The first universal reset made a universe without them with other people playing their roles, after the second they do come back and Pucci isn’t in that universe.
From what I remember if you die while Made in Heaven is active then you don’t show up in the next Universe. Irene is not Jolyne, Johnny’s whole argument with Valentine literally invalidates Part 6’s ending being happy.
I’m not angry, but I just found it funny that Araki invalidated his own ending. The ending is something I enjoy for how off the walls it goes and ends with a man getting his head crushed by effectively a hydraulic press.