Major Malfunction has gone bad. He has holed himself up inside a house and is leading an army of toys against the Army Men. The player takes control of Private Anderson and it's his job to infiltrate the house, take out Major Malfunction's army, and stop the major himself.
Army Men: Major Malfunction is a 3rd-person platformer/shooter. Shoot, dodge, and jump through over 30 missions. Each level has 10 service medals hidden in out-of-the-way places, which unlock extras. Weapons include, among others, the standard assault rifle, a mini-gun, and a bazooka, with weapon power-ups scattered around the levels.