Reading jdub28's theory on the Mario series got me thinking to a Mario game I created years ago. Here's how the game starts off (CGI): Bowser is sitting in his thrown room with Magikoopa holding Princess Peach hostage. Bowser is staring at the door and you can hear Mario jumping and killing Goombas and the like. Finally, the doors burst open and Mario guns it straight for Bowser. Before either of them can land a blow, the both get teloported into a completely dark room with only one light shining on both Mario and Bowser. Neither of them has any idea what's going on and proceed to fight.

Mario of course bests Bowser once again but before he can land the final blow, a fire ball appears from the darkness and hits Mario in the back. From the shadows, another Bowser emerges. But this Bowser is the skeleton version of Bowser from the DS game. Then another Bowser appears and it's Paper Mario Bowser. Finally, Giga Bowser emerges as well, picks up both Mario and the Bowser that was just defeated and Paper Mario Bowser opens up a portal to which they all go in to.

So that's basically the beginning of the story. One of the Bowsers figured out a way to travel to different dimensions and he started collecting all the different Bowsers from all the different games so they can all go fight all the Marios. The game would follow a new Mario who has never been "in a game before" as he hops different dimensions (From Smash, to 8-bit, to Galaxy) collecting all of the skills and power ups that have ever been while fighting all the Bowsers and rescuing all the Mario's that have been captured.

Every time he saves a Mario, he'll gain some kind of skill from them. Like, when Mario saves Paper Mario, Mario can transform into paper and use his paper skills (like transforming into a paper airplane). That's the basics of it, what do you think?