The way i see it
Ok minions of bowser who DK and diddy have never met, have just stolen the bannanas of DK, a classic thing for a DK Villan to do. Bowser will need a reason for doing this hear is how i see it playing out.
Both DK and Diddy (pick who you want to play as) fight Bowser, Bowser's minions show up in this battle helping Bowser
Cutscene, all three combantants look beat, DK looks a diddy and signals him to run, Diddy runs off. DK looks at bowser readying himself for another round, a figure in the shadows behind DK lurks behind him, DK flashes purple and colapses.
Insert scene with diddy meeting fox
Diddy and fox, fight pokemon
DK is in the SE ship his is straped in a chair with a classic brain washing hat and his eyes pinned open. He is show images of mario with a hammer, smashing barrals, DK is throwing them, Mario smacks DK with a hammer, DK brakes free from his chair, and brakes the screen.
Laughing is heard, mario is standing behind him, he goes to punch him but he disapears
As DK you fight tones of mario clones.
They all disapear, a map pops up on a moniter, with a mario icon on it, DK sees bowser coming up to see him, bowser nods at DK, DK nods at bowser, the both walk out the door the shadowy figure from before slink partaily into view we see he has a long tail.
DK and Bowser begin a search for mario