As the 8th Fleet approaches Earth, Le Creuset dispatches his mobile suits to attack the fleet. The assault is spearheaded by ZAFT's Gundam pilots, among them the wounded Yzak, who is spoiling for a rematch with the Strike Gundam. But Admiral Halberton, determined to get the Archangel safely to Earth, is keeping the ship and its pilots out of the fray.

While the Archangel crew watch from the sidelines, ZAFT's Gundams proceed to wipe out the entire 8th Fleet. At last Kira and Mu sally forth to aid Halberton's embattled flagship, but Kira is instead drawn into a fierce duel with Yzak. As the Archangel and the battling Gundams enter the atmosphere, Yzak releases his frustrations by shooting down a troublesome distraction - a shuttle filled with Heliopolis refugees, the very people whom Kira has sworn to protect.

In the aftermath of the battle with the Alliance's 8th Fleet, Rau Le Creuset reflects upon the events that led up to this point. We see how, after the "Bloody Valentine" tragedy, the PLANT Supreme Council was split between moderate and radical factions. Now the appearance of the Gundams has given new support to the radicals, and the war is likely to escalate as a result.

Le Creuset then recalls the tale of the first Coordinator, George Glenn. This genetically-engineered genius sought to usher in a new era of space exploration, but by revealing the secrets of his creation, Glenn instead split the human race into two branches - genetically-engineered Coordinators and unmodified Naturals, each regarding the other with fear and distrust.

The Archangel has safely reached Earth thanks to the 8th Fleet's sacrifice. However, the ship went far off course during its chaotic entry into the atmosphere, and instead of Alaska it's landed in the deserts of ZAFT-controlled North Africa. Meanwhile, Yzak and his fellow Gundams pilot Dearka Elsman have descended to ZAFT's Gibraltar base.

Kira, laid up in sickbay after the ordeal of re-entry, is being tended by - of all people - the Coordinator-hating Flay. Though Flay is engaged to Kira's good friend Sai Argyle, she maintains that the arrangements made by their parents are now null and void. Kira, agonized by his failure to protect the refugees, collapses into Flay's waiting arms.

During the night, the Archangel encounters a new threat - the forces of Andy Waltfeld, ZAFT legendary "Desert Tiger." Kira rushes into battle to protect his comrades... to the delight of Flay, whose intention is to use Kira as a tool to avenge her father.

Kira struggles to adapt to the desert conditions, even after he once again enters his berserker state, but the watching Andy is impressed by the skill of the Strike Gundam's pilot. With his Gundam's energy dangerously low, Kira receives some timely help from a band of resistance fighters, who lure the ZAFT mobile suits into an explosive trap. And among these resistance fighters is a mysterious young woman whom Kira helped escape from Heliopolis.