Even as Neo prepares for another attack on the Minerva, the ZAFT are on the trail of the Archangel and its crew. While Chairman Dullindal supervises the pursuit of the fugitive Lacus, Captain Talia of the Minerva receives a report on Athrun's secret meeting with Kira and Cagalli.

Yuna and Neo gather their forces around the island of Crete, hoping to catch the Minerva as it enters the Mediterranean Sea. Once again, the Orb fleet engages the Minerva in a fierce naval battle, and once again the Archangel crew decide to intervene in the fighting in hopes of preventing any further bloodshed.