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.

Claudia Peer has been captured by Zeon, which hopes that she will lead them to the location of the Psycho Zaku research facility. Daryl Lorenz brought Claudia in, but his encounter with Sojo Levan Fu has made him realize he shares her trauma. Elsewhere, the crew of the Spartan refit and rearm, and despite Io Fleming's talent for combat, his hot temper fuels lingering doubts among the Federation command that he can get the job done. As the Spartan homes in on the hidden Zeon base, secret followers of Sojo Levan Fu among both Zeon and Federation forces make their move...