I had an idea like this, What if Marvel had a Crisis on Infinate Earths?
In it Beyonder was the cause of the destruction of universes because he kept editing them until he deleted them all together.
I guess this would be the sequal, "What if Marvel did Infinite Crisis?"
In this story before being stopped, sent back to his own dimension, or destroyed, the Beyonder put a small part of himself into another character. Like say he put a small part of himself, a part of his power and conciousness, into Scarlet Witch.
Without knowing she would alter reality just by existing, almost like the Beyonder's power would radiate throughout the universe causing changes that should have never happened. (This could also explain how Wanda became so powerful she caused Avengers: Disassembled and took away almost every mutants powers.)
Other things that would be explained away would be things like:
Gwen's cheating on Peter with Osborne.
Jean Grey's return (maybe)
Onslaught
maybe Age of Apocalypse
Bucky's return, (would undo it though, I like the idea.)
The Young Avengers (wouldn't undo this either)
Darik Beast's and Holocaust's existance in our reality.
Peter Parker's power changes.
How a character dies but then comes back. (good guys and bad guys)
explain Liefield's X-Force's return story.
Ben Reily and the clone saga would definatly be part of all this.
I don't know, I'd have to think about this more.
but didn't they already do this in She-Hulk?
they had an issue where they explained away all the little mix ups, like when a character apeares when they are suppossed to be somewhere else or when a story line is alterred and such.
I never read it but I read about it.
What was the cause?