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.

Zeon ace Daryl Lorenz works to help Kara Mitchum, the brilliant designer of the Reuse P. Device, recover from the trauma she suffered in the Battle of the Thunderbolt Sector. Meanwhile, after a deadly pursuit and confrontation both in the frozen wastes of Antarctica and the black depths of the ocean, the Federation ship Spartan reaches the territory of the Nanyang Alliance. As the Spartan encounters the first Alliance border patrol units, Io Fleming learns that not all of the Thunderbolt Sector's ghosts are dead...