Gameplay alternates among three characters: Mario and Luigi, who are controlled together on the bottom screen using A and B, and Bowser, who is controlled on the top screen with X and Y. There are two main worlds: the main overworld, which is played in an overhead view, and the world inside Bowser's body, which is a 2D side-scrolling world. Although most of the game is played with Mario and Luigi inside Bowser and Bowser himself in the overworld, Mario and Luigi also have opportunities to visit the overworld via warp pipes as the game progresses. Bowser can travel between different areas of the overworld using portals known as "Chakroads", which are hidden under objects that only Bowser can destroy, such as trees and boulders. Gameplay typically alternates between controlling the brothers and controlling Bowser. Some sections involve direct interaction between the brothers and Bowser.
The battle system from the previous two games is re-used with Bowser as a playable character. Bowser's battles are similar to Mario and Luigi's, although Bowser specializes in punching and breathing fire. During Bowser's battles, he can inhale defenses and enemies from the top screen. Any inhaled enemies enter his body, where Mario and Luigi fight them. Mario, Luigi, and Bowser have their own sets of special attacks that use the touchscreen. Mario and Luigi can unlock abilities by finding attack pieces, while Bowser can earn new abilities by rescuing his caged minions or by finding living, kitten-like blocks called Blitties.
Characters have "ranks" that increase with their level. Upon reaching these milestones, that character receives a special bonus, such as an additional equipment slot, additional equipment, or being able to visit new shops. Mario and Luigi each have six ranks, while Bowser has four. The badge system from previous games has also changed; now Mario and Luigi can use certain effects by filling a meter and then touching it to activate its effect. The badge's effect, such as health recovery or raising stats, varies depending on the combination of badges equipped.
There are various minigames in which the Mario Bros. have to help out Bowser's body from the inside in order to help him progress. Examples include the "Arm Center", where the brothers hit sparklike items into a muscle to strengthen Bowser's arms; the "Leg Outpost", where they stomp on leg muscles to strengthen Bowser's legs; and the "Gut Check", where they help digest food that Bowser eats. One location, the "Rump Command", has the player accumulate adrenaline in order to supersize Bowser if he is crushed, leading to a new battle system in which the DS is held vertically and all attacks require the stylus and microphone.[3] The 3DS version substitutes button presses for the microphone but still incorporates the stylus for certain moves.