Set in C.E. 73, two years after the peace treaty between ZAFT and the Earth Alliance was signed in Gundam SEED, members of the Earth Alliance special task force known as Phantom Pain hi-jack three advanced mobile suits from a ZAFT armoury base during a meeting between Orb representative Cagalli Yula Athha and new ZAFT chairman Gilbert Durandal. What begins as a pursuit of this band of Extended Naturals by Orb refugee Shinn Asuka, Athrun Zala, and the crew of the Minerva, escalates into cataclysmic circumstances which lead to the declaration of yet another war.
Eager for retaliation, the Atlantic Federation declares war on ZAFT (who they blame for the Junius-7 drop). In defense of the oncoming nuclear onslaught, ZAFT unleashes its newest weapon, the Neutron Stampeder, against the Atlantic Federation forces.
After Zaft's ultimatum requesting Djibril, Yuuna gives the obvious lie of Djibril not being in Orb in a public announcement. Following the announcement, Zaft begins its invasion of Orb. Cagalli is given her father's will: the mobile suit Orb-01 Akatsuki, arrests Yuuna and reforms Orb's defense against Zaft. Later, the Minerva arrives and Destiny launches to confront the Akatsuki...
In Space, Lacus & Andy reunite with the Eternal and its crew. Lunamaria reports her findings from Athrun's rende-vous with Kira to Talia as Stellar's condition worsens. Elsewhere, Miriallia rejoins the ArchAngel and decodes a message that informs the group of an upcoming battle between Minerva and ORB/Phantom Pain.
The Minerva crew investigates the Lodonia Laboratory and learns the secret behind the EA's "Living CPU's." After hearing her "trigger," Stellar rushes off in Gaia to protect the lab, her birthplace.
After a misunderstanding between Athrun, Lunamaria and Meer, Shinn takes advantage of his shore leave by exploring the countryside. On his travels he stumbles across Stellar dancing on a cliff, she then accidentally falls into the sea. Shinn dives in after her. While waiting to be rescued, Shinn and Stellar share some bonding time.
After departing Orb, the Minerva is thrown into battle against an Atlantic Federation fleet. Due to their new alliance with the Federation, Orb quickly sets up a baracade of ships preventing the Minerva from retreat back to the safety of Orb territory.
As Athrun meets with Dullindal, the Dullindal-endorsed psedo-Lacus, Meer Campbell, rallies the citizens of the PLANT's look away from war and look towards peace. Later, Dullindal offers Athrun a chance to pilot the Saviour Gundam.
After the Minerva launches from Armory-1, the battle against the Girty Lue ends, for the time being. However, Girty Lue launches another attack preventing the crew from having much time to regroup.
Shinn continues to battle the three stolen Gundams. In the midst of the battle, the three Gundams work to escape from Armory-1 and rendevous with their ship, Earth's "Girtty Lue", which is under the command of the mysterious Neo Roanoake.