The Earth Alliance blames the PLANTs for the fall of Junius Seven and orders the PLANTs to disarm while they secretly prepare for an attack. In response, the PLANTs prepares their defenses. A battle starts between the two forces which almost ends in the destruction of the PLANTs when the Earth Alliance uses their new GAT-04 Windams armed with nuclear weapons. However, thanks to a new weapon, the attack is thwarted. Meanwhile, Athrun meets Gilbert Durandal.
The Earth Alliance claims that ZAFT is responsible for “the drop of Junius Seven incident” and makes an announcement to the world labeling the PLANTs as a threat. At the Alliance’s lunar base, preparations for war progress. At the meeting of the Supreme Council of PLANT, the debate becomes tangled. The mainstream opinion was to mobilize the military, but Durandal insists on negotiating for peace. But with the forthcoming attack from the Alliance, the National Defense Commission decides to mobilize ZAFT to protect the PLANTs.
Meanwhile,Athrun arrives at PLANT and asks to meet with Durandal to appeal for peace negotiations.The Earth Alliance declares war to the PLANTs and the fleet moves forward. Yzak and Dearka’s ZAKU intercept but they realize they’re fighting decoys. A secret attack fleet of Windams fire their nuclear missiles at PLANTs. The ZAFT’s battleship, however, intercepts and fires its new weapon, the Neutron Stampeder.The PLANTs were able to survive their utmost crisis.