Despite the heroic efforts of its crew, the Minerva has been unable to avert disaster, and the fragments of Junius Seven inflict terrible damage as they fall across Earth's surface. The Minerva retrieves Shinn and Athrun as they descend to Earth, then sets course for Orb in order to return Cagalli and repair the damage it has suffered in its space battles.

Meanwhile, the anti-Coordinator group Blue Cosmos is already moving to take advantage of this disaster. Lord Djibril, the new leader of Blue Cosmos, confers with the other members of the Logos secret society to plan their response.