The fierce naval battle between the Minerva and the Orb fleets has been interrupted by the sudden appearance of the Archangel and the Freedom Gundam. Cagalli appeals to the Orb soldiers to cease fighting, but her words fall on deaf ears. The battlefield descends into chaos, with tragic consequences.
After the battered Minerva withdraws to a friendly port, Athrun leave the ship to search for the Archangel and confront his former allies. As he listens to their revelations, Athrun is forced to choose between his faith in Chairman Durandal and his friendship with Kira and Cagalli.
Meanwhile, Shinn and Rey are dispatched to investigate an abandoned Earth Alliance research facility and the shocking secrets it contains. A lone enemy pilot the launches a desperate attack on the Minerva resulting in an unexpected reunion.