Cargo Commander is a played as a 2D platformer but with 3D cell shaded graphics. The player controls a Cargo Commander, the Cargo Corps' latest recruit. He works in space and must reclaim priceless cargo from containers filled with aliens. The Cargo Commander has a computer he uses to control a giant magnet. He pulls containers from space with various useful items. He also has a special Fistcannon device to drill holes in the walls and shoot the aliens and destroy spawning crystals. Aliens are like cockroaches, they infest containers and are dangerous.