Jon Negroni would like to blow your mind with his theory on how all the Pixar films are telling one massively epic story:
Yes, Boo is the witch from Brave. She figures out how to travel in time to find Sully, and goes back to the source: The will-of-the-wisps. They are what started everything, and as a witch, she cultivates this magic in an attempt to find Sully by creating doors going backwards and forwards in time. […]
Obsessed with finding Sully, Boo traveled across the Pixar universe using doors. So Boo went back to the Dark Ages, probably because she could use plenty of wood there for her experiments or to study the will-o-wisps. We know that her first encounter with Mor’du ended with her turning him into a monstrous bear, but he regresses. She probably wanted to turn him into a bear because Sully resembles a bear, and she is still trying to figure out where Sully comes from. Does Boo ever find Sully? I like to think so. He surely reunited with her at least once as a child at the end of Monsters Inc. but eventually he had to stop visiting. But her love for Sully is, after all, the crux of the entire Pixar universe. The love of different people of different ages and even different species finding ways to live on Earth without destroying it because of a lust for energy.
The only problem with this theory is that it is based on the assumption that Pixar actually has been making each movie to be a small piece of a greater whole. I suspect, like ABC’s TV show ‘Lost’, that Pixar is just making it up as they go and having fun by throwing in Easter Eggs from one movie to the next.
Still, I want this to be true — Pixar’s actual intention — more than anything.