From the Super Mario Wiki
A Shroob missile is a weapon used by the Shroobs in Mario & Luigi: Partners in Time. After the babies rescue Mario and Luigi from the Shroobs and are in the Koopa Cruiser with Baby Bowser and the Koopa Troop, Princess Shroob then summons a Shroob missile from Shroob Castle to finish them off. It smashes the Koopa Cruiser successfully, due to Baby Bowser being all out of ammo to destroy the missile itself. The Koopa Cruiser then crashes and lands in Baby Bowser's Castle. No Shroob missiles are seen for the rest of the game.