The Koopa Commander, as his name suggests, is the commander of the Koopa Troop army. He's only seen in HTF Origins, where he's the boss of Volcanic Jungle. There, he's seen driving what appears to be a mech combined from King Tank and King Plane.
His mech's only weak point is the red turret on the bottom part of the mech, which is used to fire red energy shots. Aside from energy shots, he can also fire missiles.