While the Allied Nations were still recovering from the war in Cosmo Land, the Black Hole Army had already recovered and has decided to launch a large-scale invasion on Macro Land. Along with the original Black Hole army's commanding officers, four new COs were recruited, under the command of Sturm.
Sturm orders each Black Hole CO to invade and capture each of the four continents controlled by the four other armies from the original game. The four allied armies must now work together to drive Black Hole out of their world once and for all.