This story starts in the year 3199, when a mighty enemy attacks the Milky Way from a neighboring galaxy. The enemy engages the combined forces of the Milky Way, an Alliance of many stellar nations, and defeats them one after another.

The remaining Milky Way Alliance forces are reduced to just six fleets. After the Alliance headquarters is destroyed, and when the collapse of the central Milky Way Alliance is imminent, the Great Yamato Zero surprises everyone and embarks on a mission to assist the Milky Way Alliance in one last great battle.