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.

Nanyang Alliance forces begin preparations for Operation Maitreya, their attempt to seize the Republic of Zeon's Solar Ray weapon. The wreckage of the Side 4 Moore colony provides the ideal training environment for the assault, but Io Fleming and the Newtype Lily--piloting the cutting-edge Zeong MS and equipped with the Psycommu system--are closing in. Although the vast fields of debris give excellent cover, the Alliance deploys a new Psycho Zaku pilot to hold off Io and the oncoming Earth Federation fleet. As the combatants close to contact, the sound of jazz once again returns to the Thunderbolt Sector...