Advance Wars begins with the nation of Orange Star thrust into war when its neighbor Blue Moon, under the brash commanding officer Olaf, suddenly launches an invasion. As tactical advisor to the Orange Star army — appointed by its de facto leader, Nell — the player guides the war effort across four nations, choosing which of several Orange Star COs to advise: the earnest Andy, the powerful Max, or the swift Sami, each with their own strengths and weaknesses, and each capable of sending the branching story down different paths.
As the conflict widens, Orange Star's CO Andy is mysteriously accused of unprovoked aggression by Green Earth's CO Eagle, and the neighboring nations of Green Earth and Yellow Comet, fearing invasion, declare war of their own. But suspicions begin to crack: COs like Drake and Sonja come to realize that "this entire conflict has been orchestrated from the beginning," and that Andy was never the true aggressor. At last the real enemy is revealed — the shadowy Black Hole Army under the ruthless Sturm, who used a CO clone of Andy to sow war among the four nations, hoping to confuse, weaken, and conquer them all. With the truth exposed, the four countries finally unite to drive Black Hole out of their land for good.