The reason why Jojo takes place in two universes is that the original universe's timeline came to an end in part 6. Time was ...

JoJo's Bizarre Adventure now spans nine parts, and the final battles at the end of each part have provided some of the most emotional, hype, and simply fun moments in the entire series.

Fans of Jojo's Bizarre Adventure may not be aware of the story which ties parts 3 and 4 together, but it's absolutely worth reading for any Jojo fan.