* When Bomb Man was singing in the corner, why was "I'm Just a Love Machine" chosen, instead of, say, "Sex Bomb"?
** To avoid using the word sex, and/or to use the word machine.
* Try as I might, I can't figure out how they got Mega Man's AI back when it was blown out of his arm and how they dealt with the Vic AI that had to impersonate him.
** Remember that 'fucking Ran recolour', Random? Not just a one-shot Ran-Bomb gag. And WordOfGod states that Dr. Light removed Vic offscreen at some point.
* The epilogue confuses me. Is [[spoiler:the Shadowy Author really the Author from the future, come back to the past to avert a time paradox or something?]]
** [[BluntYes Yes]].
*** Well, technically, yes and no. Basically, Shador is the author of another universe extremely similar to ours, and [[FanWank may be a Dave Anez from another universe parallel to ours.]] As dumb as it sounds, if you watch the Catclysm movies, at multiple points, the characters are referred to by their Japanese names (Rock, Forte, Blues), which was previously used to differentiate the Rockman Universe from the Megaman Universe, showing that any split is likely intentional. This means that Shador is another author trying to prevent the Cataclysm in at least one universe, specifically the one closest to his. [[FridgeBrilliance This may also be why he "cares" for the Rockman Universe: it reminds him of his own universe as well.]] Anyways, this would mean that, rather than the Author "becoming" Shador, he would simply become an entity greatly SIMILAR to Shador. This could imply that this whole series of events, including The Cataclysm, Bob and George's entrance, and even Shador merging with George is one long cycle, repeating with a new universe every time until this universe, our universe, broke out of it. Or, you know, [[OccamsRazor this could be over-thinking it and Shador caused a time paradox.]]
* At the end of the Epilogue, it says that after Zero accidentally told Dr. Wily that he would end up killing everyone, Wily decided to never activate Zero and the Cataclysm never happened, causing everyone to go live in Acapulco to avoid a time paradox. So how come Zero is with them in Acapulco in the end? Shouldn't he never have been activated?
** Wily probably programmed Zero with fake memories of killing everyone, and then set Zero on a timer to wake up ''later''.
** Could be one from a universe where everything went down as normal. Alternatively, just say "I hate time travel" and leave it at that.
** Additionally, presuming Bob and George went home at the end, how are they in Acapulco? The early reveal of the Cataclysm shouldn't have affected them, since according to the epilogue they're home and never return.
*** The epilogue also says everyone died in the cataclysm. I just took that to mean that everything up to that point (including Bob and George never returning) was what ''would have'' happened if they hadn't gotten smart.
*** Actually, assuming the Catclysm took place VERY shortly after the ending, it's possible two of the devices destroyed would have been the time machine and the dimensional transportation device (if they have one). OR nobody knows how to operate them aside from the main characters. Or maybe [[OccamsRazor Dr. Light decided in that hypothetical that he was sick of time travel like everyone else.]] Any of these would explain why the Megaman characters could never contact them again in that universe.