As the Alliance gathers its forces at Panama in anticipation of a major ZAFT attack, the Archangel is reassigned to the Alaska base's defensive garrison. Natarle, Mu, and Flay receive transfer orders and bid farewell to their comrades aboard the Archangel.

The long-awaited Operation Spit Break begins, and the true target of the offensive is revealed: rather than attacking Panama, ZAFT is striking directly at the Alliance headquarters in Alaska. Le Creuset enters the base ahead of the main force, confronting Mu and taking Flay prisoner. Back in the PLANTs, Lacus entrusts Kira with a powerful new weapon.

As the Alaska defense forces fight desperately to hold back the ZAFT assault, Mu returns to the Archangel to tell the crew that they're being used as bait for a deadly trap: the Alaska base has been abandoned, and its lowest levels house a Cyclops System, a massive microwave array that will destroy everything within ten kilometers of the base.

Suddenly, a new combatant enters the battlefield. Kira descends to Earth in the mighty Freedom Gundam he received from Lacus, and quickly clears a path for the Archangel. While the ship races to escape the Cyclops System's area of effect, the Alliance leaders activate their trap. The Alaska base vanishes in an inferno of destruction, consuming Alliance and ZAFT forces alike.