Exodia is a pretty powerful foe so it’s safe to assume that a few good energy blasts would take Bowser down for the count. Bowser has access to his Giga Bowser form, but that just won’t be good enough to defeat Exodia. Exodia can knock away Bowser’s fireballs and he would likely be superior in physical strength. Bowser is just out of options. Exodia wins.