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At the climax of fight against Pucci, many of our protagonists have died after he activated Made of Heaven, barring Emporio. He was brought over to the new universe, much to his confusion. To tie up loose ends, Pucci pursued Emporio in Green Dolphin Prison, ultimately ending up in the ghost room. There, Emporio assimilated Weather Report's stand disc, and used it to remove the oxygen in the room suffocating Pucci and finally killing him.

After Pucci obtained Made in Heaven, he began accelerating time for all non-living things in the universe. Due to this, the whole world experienced various strange phenomena. These includes corpses rotting quickly, vehicle moving faster than a person could operate leading to widespread accidents, the sun and moon moving at fast speeds across the sky, and oddly specifically, every manga artists being unable to keep up with the weekly release schedule.

In her attempt to escape prison and stop the scheme of Pucci, a priest who is a follower of Dio, Jolyne have various allies to aid her. These includes inmates such as Ermes and F.F from the female ward, and Anasui and Weather Report from the male ward. There is also Emporio, a child who was born in prison whose stand creates a "ghost room" for the team to gather.