At the end of Jojo Part 6: Stone Ocean, did Emporio get sent to a parallel universe? Is this the same universe that SBR and JJL then take place in? The wikia says that the universe is reset. What really happened? I'm so confused...
Some years ago I shared your confusion, and I kept thinking and thinking until I found an answer I was satisfied with. I also wrote this "answer" in an italian forum I was part of at that time. To be fair, it did not receive very much attention, but I want to translate it because I think it could be of some help (I doubt it to be correct because I believe H. Araki's brain creations are too much for anyone to understand).
Here I go:
Father Pucci makes the universe collapse by means of the powers of his Made in Heaven. Then, the universe rises again for another cycle of life. The interesting fact, which H. Araki himself explains to us, is that this new cycle will be exactly the same as the one before except for the fact that all the living beings that are actually alive when the collapse takes place will return in the second cycle of life with full knowledge of their future. This consciousness of the future is how Father Pucci believes happiness will be achieved by mankind.
The new history of the universe will be written in such a way as to preserve the faith of who was alive before the first collapse operated by Father Pucci through Made in Heaven. Details will obviusly change, but the main part of their faiths will be unaltered. As for the deads, something similar happens in the sense that their new lives will be somehow "connected" with the lives of those with whom they were connected in the first cycle, but there will be no clear knowledge of their faith for them.
It is clear that Father Pucci is the only living being which is outside of the "written faith", and he can move arbitrarily in the cycle of the new universe because of the gravitational powers of Made in Heaven. Since Father Pucci knows that Emporio is alive before the collapse, he decided to close the situation once and for all, and goes back to the prison (during the second cycle of the universe) in order to kill the little guy.....and this is where Father Pucci makes his big mistake.
Emporio manages to survive Father Pucci's threat precisely because Father Pucci is immune to Made in Heaven powers. Indeed, we know that the details of the lives of who was alive before the first collapse may change, and this clearly allows Emporio to have some kind of mental and physical freedom with which he is able to think to a plan to kill Father Pucci. Furthermore, we know that Father Pucci's faith is completely open, there is no predestination for him because it is his will to actively keep using his powers the reason of everyone else's fixed faith. This means that, even if Father Pucci can litterally decide the faith of the universe, nothing prevents him from dying like the idiot he surely does not want to be.
Then, he dies, of course.
Before dying, Father Pucci decides to accelerate Time again hoping to prevent the result of Emporio's plan (his death) before it actually realizes. All he succeds to do is to set a third cycle of the universe, a cycle of which he will no longer be part of. However, Emporio was alive at the time of the second collapse, hence, he will be fully conscious in the third cycle, and thus he tries to reconnect with the group. He finds Irene and Anakis, the "alter-ego" of Jolyne and Anasui, who, however, do not have Emporio's knowledge of their faith and are not able to remember him (they were dead before the first collapse).
In this third cycle, Father Pucci is no longer there because he died in the end of the second cycle, and thus we may safely assume that there will be again a lot of freedom for everyone. Accordingly, I believe that SBR takes place in this third cycle, because, if it had took place during the second cycle, there would have been Father Pucci somewhere in the universe, and this would have made the plot of SBR meaningless with respect to the "fixed faith" imposed by Made in Heaven.
Now that I wrote it again, I feel better. Please, forgive my english and let me know what you think.
Remark At the time of my writing now (26 January 2019), I have not yet started reading JoJolion (part 8), hence, I do not know what happens there. The following edit has been suggested by someone who is reading JoJolion, and I thought it could be meaningful to add it because it seems to disprove my "theory" on the end of Stone Ocean. However, I reserve my right to re-edit this answer once I read JoJolion and I have thought about it, and I warn people who have not read JoJolion that the following suggested edit contains information that may be perceived as spoiler. End Remark
Peer edit: In JoJolion (part 8), the theory that the Steel Ball Run universe takes place in a cycle of Made in Heaven was disproven, as the complete Joestar family tree is shown, and there is no Jotaro nor Irene.
This is because the Steel Ball Run universe is a completely different universe. The third cycle of Made in Heaven is its own universe. The SBR-verse and Ireneverse have no correlation whatsoever.
My interpretation was that civilizations came and went with time's acceleration, effectively resetting the universe. The next part steel ball run arguably has a major plot point related to this.
I'd guess there's a decent article somewhere.
Here's a quote from the jojo wikia. (http://jojo.wikia.com/wiki/Alternate_Universe)
Made in Heaven increases the speed or rate of the flow of time; achieved through its ability to control the gravitational forces of the earth, moon, and seemingly the entire universe (in reference to aspects of the theory of relativity).
As time continues to travel, the universe will hit a "vanishing point", and a new universe will be created, where everything repeats itself, according to "fate".The Stand's user may then alter the characteristics of the universe and the fates of the people in the recreated universe and create the perfect world they desire.
In the story, just after Enrico Pucci's death at the hands of Emporio Alnino and the Stand Weather Report, the universe completes a second cycle. In this renewed world, characters of seemingly very similar identities to Jolyne, Hermes, Anasui and Weather Report fortuitously gather in Emporio's proximity.
My theory on this is that Pucci's speed ability creates an alternate universe. This would make sense because we clearly figured out the Johnny Joestar is the alternate Universe Johnathan. Which is confusing why they didn't continue with the original people. I mean we don't know if Jotaro and Jolyne are even dead because we are left on a cliff hanger. I mean we are still waiting for part 9 which I believe will be sometime this month because of the new Part 6 anime coming out this March sometime.
I know that this is super late however I just finished all the current Jojo story a week ago or so and I was thinking about part 6. To be honest, this was the only part that I disliked. The end left me thinking if this was a good ending or a bad ending for both the Joestars and Pucci.
Well anyway, on to the answer.
What I understood is that the ending isn’t in a alternate universe at all. With Father Pucci’s stand, he was able to increase the ‘speed of time’ kinda. This made it so that all life and remains of life on earth were destroyed. Like, he lessened the time it would take for life to meet it’s demise. Then, life was reborn, however everything followed the same fate. We end up at the time around when Emporio met Jolyne in her “old life”. While somethings have changed, to me it seems to me that Pucci failed. As shown at the very end, the ‘future’ Jolyne has the trademark Joestar birthmark.
The only thing I still don’t get is why Emporio was uneffected by Pucci’s stand. Either that or I forgot and I’m too lazy to reread.