In the Universal Century year 0079, the space colony known as Side 3 proclaims independence as the Principality of Zeon and declares war on the Earth Federation. One year later, they are locked in a fierce battle for the Thunderbolt Sector, an area of space scarred by the wreckage of destroyed colonies.

The forces of Levan Fu's Nanyang Alliance have gained control of the Solar Ray and are moving it into position. By clouding the minds of the Federation's Konpei Island fleet personnel with his Newtype powers, Levan Fu has misdirected the Federation in order to attack the Zeon colonies. The Beehive II is now the only Federation unit able to intercept. Bianca launches a desperate mission to take out the BYG-ZAM, and old enemies Daryl Lorenz and Io Fleming cross swords once again...