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 Federation assault ship Spartan sets course for the Nanyang Alliance's Psycho Zaku manufacturing base in the Taal volcano and begins preparing for full-scale combat operations. Io Fleming and the members of the Trust Squadron bond before the struggle to come, as Daryl Lorenz and his crew of Zeon defectors do the same. On the Spartan, Director Humphrey lays out the challenges of the assault--in addition to the Psycho Zaku the Federation will be facing Alliance forces under the psychic control of Sojo Levan Fu. However, Levan Fu will not be the only Newtype in the looming battle...