"Ugh..." Mario groaned as he sat up, he rubbed his head until he noticed his hand wasn't a hand, it was a Tepig's footprint "Huh?!?" Mario panicked. he quickly ran to a river and looked down at his reflection. It was true! He was a Tepig wearing a blue neckerchief! "Ahhhh!!!" Mario yelled. He circles around himself "I must be dreaming.. this can't be right..." He then looked over at Sonic, who had become (name either a starter pokemon, pikachu or riolu that you want to be). (whatever Sonic was) was wearing a red neckerchief "Sonic! Get up! this is an emergency!" Mario shouted to the hedge- er- pokemon.
...
Meanwhile, halfway across tis strange Pokemon world, Bowser let out a groan. He stood up and breathed smoke, which was weird, he never did that. Like Mario, he went up to a lake, and saw that he was a Torkoal, only unlike Mario, he didn't see anyone he knew of, no Eggman in sigh, no nobody. He was on his own. Grumbling, Bowser walked off
Mario, Sonic and friends have been scattered across the world of Pokemon Mystery Dungeon, the world where only Pokemon live. Mario and Sonic become an exploration team and travel all across the world trying to find the answer on how to get back home, and how they got there. Eggman and bowser are here too (Bowser became a Torkoal as you saw, but eggman can be whatever as long as its not a legendary, but it would be histerical if he was an Exeggutor XD). They will team up with the others at a later date, but of course they're all Pokemon too, meeting all kinds of new Pokemon, having adventures, finding treasure and stopping criminals all on their quest to get back home)(when it comes to what pokemon everyone became, i'm trying to be logical, except with mario and sonic, they need to be either a starter, pikachu, or riolu, like the real mystery dungeon game)