The Orb Union space colony, Heliopolis, is attacked by ZAFT, despite its neutrality since the beginning of the Bloody Valentine War. Kira Yamato accidentally sees the Earth Alliance's new prototype mobile suits, which have been secretly constructed at the Heliopolis Morgenroete factory. He encounters his childhood friend, Athrun Zala, now a ZAFT soldier as one of the attackers.

ZAFT is able to steal four of the five G Project prototype mobile suits, leaving only the GAT-X105 Strike. With Murrue Ramius unable to pilot it effectively, Kira pilots the Strike and defends Heliopolis against the invading ZAFT forces to protect his friends. Ensign Natarle Badgiruel takes command of the new mobile assault ship Archangel with the surviving crew members.

Lt. Murrue Ramius takes over as captain of the Archangel and Kira and his friends are detained for seeing top secret military weapons. Rau Le Creuset is determined to capture the Strike after seeing how well it moved and sends out mobile suits to retrieve it. Disobeying orders, Athrun also dispatches so he could confirm if Kira is the one piloting the Strike, but when he finds his answer, Heliopolis crumbles as it sustains too much damage.