See, your two mustachioed heroes are doing the bulk of their familiar 2D adventuring inside Bowser's body (hence the name), while Bowser himself will be embarking on his own adventure, presented in an isometric, Super Mario RPG-esque fashion. Just as you had to control Mario, Luigi and their baby counterparts simultaneously in Partners in Time, you'll be controlling Mario, Luigi and their overworld/adversary Bowser simultaneously in Inside Story.
Here's whats so brilliant about this formula -- as you travel around the world as Bowser, you encounter problems during your journey which require the help of your interior plumbers. In the demo we played, Bowser needed an extra burst of strength to pull an entire island inhabited by a single French blockhead (yes, it still retains the series' quirky brand of comedy). Mario and Luigi made a quick trip to one of his arms, fighting off viral Blorbs in search of his biceps, which they pumped up by returning volley after volley of electric orbs using their trusty hammers. After adequately pumping him up, Bowser had the strength to move the landmass.
This gameplay function works both ways -- a long hallway features bone fragments that serve as barriers to the Mario bros' progress. Forcing Bowser to drink water until he feels "all sloshy" fills the chamber, causing the bones to float safely out of the way.
We can't wait to see how these two different worlds interweave. As evidenced by the series' extremely pithy dialogue, the game's creators are probably clever enough to come up with a number of scenarios where the miniscule plumbers and dino-turtle-monster have to work together. Combining said cleverness with the series' tried and true action-oriented RPG gameplay is going to create what could be the most entertaining chapter in an already entertaining series.
We're just hoping Mario and Luigi's internal exploration doesn't go south, if you know what we mean