In battle Commander Shroob first sends in three Support Shroobs carrying a Shroob-omb. The four Mario Bros. need to destroy the two Shroobs farthest away from them to cause the bomb to roll offscreen. An explosion is heard and Commander Shroob is Knocked into the arena.
The commander himself has two attacks, The Generic Shroob attack of shooting orbs of energy at the heroes (He spins to attack Luigi and and holds a spark to attack Mario) and an attack where a bunch of generic Shroobs rush in towards the Bros.. As they approach the Commander he twirls them towards one Bro., or launches them in the air toward one. Both can be countered by hammers.