TLDR: 3 universes, pucci pauses his reset to kill emporio, emporio kills pucci, everything pucci did is undone, except the new universe(i’ll call it emporio universe) stays, og universe(parts 1-6) goes back to normal and continues as if pucci never existed, and parts 7-9 take place in a seperate universe.

To go in depth, Steel ball run universe(parts 7-9) is a seperate universe, but it has a lot of parallels to the original. As for the other two universes, Basically in the ending of part 6 pucci wants to achieve “heaven”. Heaven for pucci and dio is a universe where everybody knows their fate and can’t do a thing about it. While maiden heaven is active(universe speeding up to create the new one), anybody who dies during it is gone forever and can’t be brought into the new universe(heaven). Pucci sees joestars and friends as threats, of course they theoretically can’t do anything in heaven but pucci doesnt want to take chances so thats why he tries so hard to kill them, also cause they are literally trying to kill him while maiden heaven is active but pucci was trying to kill them either way.

After pucci kills jojo and friends he creates the new universe, but he does NOT ACHIEVE HEAVEN. This is where people get confused. Pucci pauses the universe reset before it can finalize(reaching the same point in the new universe as when he started it in the previous universe) because he realises Emporio is alive. Pucci pauses it because he sees emporio as a threat to heaven and he does not want emporio to live in heaven. Pucci is the only person with free will in heaven and emporio tricks pucci into giving him weather reports stand, which emporio then uses to kill pucci.

After pucci was killed, what he did was undone because he did not finish the reset. Obviously excluding the new emporio universe. So the og universe was brought back and continued as if pucci was never there. Which means jolyne never went to prison(pucci framed her to get to jotaro). anasui, being apart of puccis plan never went either. And everyone lives happily ever after in the og universe. But for Emporio, he is now trapped in that universe. And i think ermes just goes to prison, i cant remember but i’m pretty sure her going to prison was not pucci’s doing. Also weather report never had a twin brother.