From the Super Mario Wiki
The shell defense is a counterattack that Bowser learns in Mario & Luigi: Bowser's Inside Story and Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey. The move is meant to counter enemies who attack Bowser from above rather than the side. Unlike other countering moves, the shell defense does not directly cause damage to enemies; rather they simply hit Bowser's shell and bounce off, sometimes harming them from the spikes on his shell. In some cases, enemies who hit Bowser's shell will become vulnerable to Bowser's punching counterattack. Due to Bowser crouching to use this move, it also serves as a way to duck under enemy attacks that cannot be punched back. Bowser is able to use this counter shortly from the beginning of the game, when he is taught by Broque Monsieur during his fight with Broggy in Plack Beach.