Bob and George/WMG

Bombman was a fireworks machine
He was there to light up the night sky on the Fourth of July (despite being Japanese... or something)
 * Substitute "Fourth of July" for "Japanese Festivals" and the Japaneseness doesn't matter.
 * It's funnier if it's for the Fourth Of July despite being Japanese.

There are hardly any theories here because the human mind can't think of anything more insane than the actual plot of Bob and George
This is just shooting in the dark, but it is possible that the human race has peaked in the field of insanity.
 * ... Is that a challenge I hear? ::evil grin:: Right, mad theories, GO!
 * The reason there's hardly any theories here is because they're all on the site's forums. There's some crazy shit in there, let me tell you.
 * Then I think it's high time we go into the forums and bring that so called "crazy shit" here so it can be remembered for all eternity.
 * There are no theories because the author explains a lot in his commentaries.
 * You want insanity? Okay then.
 * Every character is actually made of radioactive cheese from highly evolved cows.

The Drawn Comic Will Actually Be Made.
Well I can hope.
 * Or fear.

IF Bob Ever Has a Kid...
The child will have control over his * own* element: Portals. That's right- after being sent through the multiverse like a damn ping-pong ball, borrowing the power of a * god*, and spending an awful lot of time out of his home dimension, Bob will have absorbed enough ot the dimensional energies to pass it on. God help us all.
 * This could be tempered by instilling in any of his children his hatred of time travel.
 * Wrong sibling - it's George who hates time travel, not Bob. Bob would probably enjoy the chance to mess around with our past again.
 * Only one kid gets it- if he has more then one, the other gets something silly, just for horrible contrast.
 * Bob's kid will get dimension hopping. George's will get Time Travel. When George finds out, he will go, "No! We will not have any of that shit!"

The Cataclysm never happened in the first place
Just faking their deaths wouldn't stop a paradox.There'd still be a matter of the destruction caused by it and Promethus remembering it.To make sense of it all Dr Wily programmed the events of the Cataclysm into Zero,made a copy of his mind into the virus and left the capsule in the abandoned mine shaft to be found a century later.Promethus copied his memories of the Cataclysm into Proto Man,which would activate decades later so that Proto Man would believe the Cataclysm would happen.As for Auto,a copy of him was made with Cataclysm memories because everyone hates Auto

The Alternate Mega Man Universe was supposed to have a Cataclysm
The appearance of Alternate Bob and George diverged it from the original AMMU like how Bob diverged the Rockman Universe

The Cataclysm did happen,but it was changed
And it turns out paradoxes don't end up destroying universes

The Cataclsym did happen, and will happen
Necessary to stop universe destroying paradoxes

The Cataclysm did happen,it was changed, and..
The universe itself was destroyed from a paradox

The Shadowy Author's identity is...
The Author of the Rockman Universe:That universe was a sprite comic by a parallel version of our universe,where the Mega Man franchise remained incredibly similar to its original Japanese version.The Rockman Universe suffered through the Cataclysm seen in the incomplete Cataclysm movies,and the Shadowy Author went back in time to stop the events.Bob ended up screwing things up, so yeah..

The alternate future version of the Author:When the Cataclysm was averted,it merely diverged the timeline into the unaltered timeline and the new one. The Shadowy Author was the future Author of the original timeline,and left at the divergent point.

Bob and George also went to Acapulco with the others at the end.
According to the epilouge, before the twist, Bob eventually was killed and George never was able to return to the Megaman universe. However, since it's revealed that everything that we were told in the epilouge was in fact FALSE, and that the others ran away to Acapulco, there is a chance Bob and George also went too.