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.
As the ArchAngel crew scrambles to stabilize their ship, Cagalli rescues an incapacitated Kira. Aboard the Minerva, Shinn gloats to Athrun about his victory. Dullindal decides to make his way towards Earth to present two new Gundams to Athrun and Shinn...
Kira, Lacus and the remaining Arch-Angel crew embark on their old vessel and depart, but not before Kira rescues Cagalli from her wedding to Yuna.
After a trip to the Mendel Colony, Lacus and the Eternal's location is discovered by ZAFT. Just when it looks bleak for the Eternal, Kira comes to the rescue...
Lacus stumbles across Meer's diary. Dullindal official announces his Destiny Plan to the world...
As Dullindal plays a lonely game of chess, he reflects upon the past and the philosophy of his dear friend, Rau Le Crueset.
The Minerva arrives at Orb. While the crew enjoys some downtime. Cagalli learns some unsettling information about the future of Orb. While Athrun decides to return to PLANT once more and meet with Dullindal.
As a last ditch effort, the Mireva uses is Tanhäuser to break up the remaining chunk of Junius-7. Unfortunatey, several of the pieces fall to Earth destroying several of Earth's cities. The battle-damaged Minerva makes its way to Orb to re-supply and to drop Cagalli off.
Athrun, now a member of the super elite ZAFT task force FAITH, returns to the Minerva. Once aboard, he delivers the Minerva's new mission to Talia.
With Milliaria's help, Athrun is able to meet up with Kira and Cagalli to discuss recent events.
The Minerva and ArchAngel work to stop the Destroy Gundam and its destructive rampage through Europe. Shinn is shocked to learn that Stellar is the unit's pilot.
Orb decides to ally itself with the Atlantic Federation, much to Cagalli's dismay. While about the PLANT's, Athrun recieves some help making his decision from some old comrades.
In order to save Stellar's life, Shinn brings her back to Neo.
Shinn and Rey both recieve pardons for freeing Stellar, a Prisoner of War, much to Talia and Athrun's surprise. Meanwhile, a revitalized Stellar pilots the EAF's new Destroy Gundam and wipes out several villages on the Russian front.
Shinn, swearing vengance on Kira, studies up on FREEDOM with hopes of defeating the Gundam that killed Stellar. Meanwhile, the Earth Sphere is thrown into chaos as Dullindal announces to the world that Logos is behind the war and the hatred.
After his less than warm reception to Dullindal and his new Gundams, Dullindal decides that Athrun will only hinder his goals. With Special Ops soldiers after his life, Athrun decides to, once again, leave ZAFT.
ZAFT leads an offensive on the EAF's Heaven's Base in hopes of defeating Logos.
Athrun launches into battle with his new Gundam, Infinite Justice, and tries to reason with Shinn. Meanwhile, Djibril makes his move to escape Orb.
All hell breaks loose in a three way battle between the Minerva, Orb/Earth fleets and the ArchAngel.
Cagalli and Shinn's duel is interupted by Kira's appearance on the battlefield. As Kira challenges Shinn to a rematch in his new Gundam, Cagalli goes to Orb's national defense HQ to interrogate Yuuna about the location of Djirbil. Aboard the ArchAngel, Lacus presents Athrun with a new Gundam.
The confusion brought on by Lacus' speech soon turns to anger as Djibril fires the Requiem and wipes out a small cluster of PLANT's.
The Minerva leads an attack on Djibril's moon base as Djirbil prepares for the Requiem's second movement.
Aboard the Minerva, Rey works to quell Shinn's doubts about the Destiny Plan. As Orb and the Kingdom of Scandanavia announce their refusal of the plan, Dullindal uses Requiem on the EAF's Althea Base...
Kira and Athrun face off against Shinn and Rey as the battle of Messiah continues...
Kira and Athrun work to destroy Requiem's first relay point. As Orb forces close in on the Requiem, Dullindal reveals Messiah's secret weapon.
With the help from a young rebel, the Minerva team is able to take out the EAF's Lohengrin and end their oppression on a town.