Kira and Cagalli go to the city of Banadiya, where the ZAFT base is located, to buy food and supplies for the camp. The two accidently meet the “Desert Tiger” Andrew Waltfeld when they are eating lunch and are baffled over his overly friendly manner.

Waltfeld, the “Desert Tiger,” attacks Tassil, the town where the rebels reside. Missiles fired from the BuCUEs engulf the town in flames. However, Waltfeld’s men gave the citizens a warning before the attack, so there were no casualties.

With the help from the “Desert Dawn” guerillas, Strike Gundam was able to repulse the attacking force of the BuCUEs led by Waltfeld. After daybreak, other members of Desert Dawn guerillas join the Archangel.

The Archangel landed on the desert in North Africa. Without any time to relax, they are attacked by the ZAFT forces at night. They are the elite ground squad led by Andrew Waltfeld, also known as the “Desert Tiger.”

Upon atmospheric re-entry, to save Strike Gundam after the battle with Duel Gundam, the Archangel was diverted off course and have ended up in Africa, which is ZAFT territory.

On the Earth’s orbit, a fierce battle has started between the Alliance’s 8th Fleet and the ZAFT forces. Although the Earth Alliance was superior in numbers, Rau Le Creuset’s troops, with GINNs and all 4 Gundams, destroy the Alliance’s craft one after another.

The Archangel finally rendezvous with the Earth Alliance’s 8th Fleet. Lost in busyness, as if to be reluctant to part from it, Kira does maintenance on Strike Gundam when Murrue comes and thanks him for all his hard work so far.

As promised, Kira returns to the Archangel. A hearing is held but the issue handing over Lacus to ZAFT without permission is disregarded through the good offices of Murrue.

The Archangel was able to stop the attack from ZAFT ship Vesalius by using Lacus Clyne as hostage, but the shock was most detrimental, witnessing an entire fleet destroyed before the crew’s eyes.

11 months have passed since the Earth Alliance and ZAFT (Zodiac Alliance of Freedom Treaty) entered into war. In L5, on the resource satellite Heliopolis of the neutral nation Orb… On this colony, Industrial College student Kira Yamato, as usual, heads for the lab where he accidentally gets involved in a Gundam extortion plan by the invading ZAFT forces.

The Atlantic Federation and its allies declare war on the PLANTs in response to the fall of Junius Seven. Although Chairman Durandal still hopes for a diplomatic solution, the ZAFT forces are mobilized to defend the PLANTs.

Once the Minerva arrives in Orb, Cagalli resumes her duties as Chief Representative. Her prime minister, Unato Ema Seiran, tells her of the damage caused by the fall of Junius Seven and urges her to approve an alliance with the Atlantic Federation.

Despite the heroic efforts of its crew, the Minerva has been unable to avert disaster, and the fragments of Junius Seven inflict terrible damage as they fall across Earth's surface. The Minerva retrieves Shinn and Athrun as they descend to Earth, then sets course for Orb in order to return Cagalli and repair the damage it has suffered in its space battles.

The Minerva launches its mobile suits to support Yzak and his demolition crew. Shinn, Rey, Lunamaria, and Athrun join the battle against the mysterious group who have sent Junius Seven falling towards Earth.

Having eliminated Requiem's first relay station, the Archangel and Eternal rush to the moon to join the attack on the Daedalus base, only to find their way barred by the mobile fortress Messiah. Kira tells Athrun and the Archangel to continue on and destroy the Requiem cannon, while he and the Eternal stay behind to deal with Messiah.

Aboard the Minerva, Chairman Durandal receives shocking news. The ruins of Junius Seven, the PLANT that was destroyed in the infamous Bloody Valentine incident and where the armistice treaty was later signed, have left their stable orbit and begun falling towards Earth.

By using the Requiem cannon against the Earth Forces' Arzachel base, Chairman Durandal has shown that he will destroy anyone who stands in the way of his Destiny Plan, and it is clear to all that Orb is his next target. The Orb space fleet and its allies scramble to attack the Daedalus base before Requiem can fire again, while the Archangel and Eternal attempt to destroy the cannon's first relay station.

The fragile peace is shattered, as the world is once again thrown into turmoil by the announcement of Chairman Durandal's Destiny Plan. To eliminate conflict and secure eternal peace and happiness, Durandal intends to use DNA analysis to assign every human being to his or her proper role in life, creating a regulated society without free will or desire.

Lacus and her companions return to the Archangel, carrying with them the body of Meer Campbell. Now that Meer has given her life to save Lacus, Athrun is ashamed to realize how little he knew about her.

With the Daedalus base captured, Lord Djibril eliminated, and the Requiem relay stations safely under ZAFT control, Chairman Durandal's victory now appears complete. As the world awaits Durandal's next move, the Archangel heads for the free lunar city of Copernicus to monitor the situation.