The battered Minerva retreats to a port on the Sea of Marmara to repair the damage it sustained in the Dardanelles battle. Troubled by the chaos his former comrades created during the fighting, Athrun decides to leave the Minerva and go in search of the Archangel so that he can talk to Kira and the others in person.

The Minerva receives orders to investigate an abandoned Earth Alliance research facility in the area. Shinn and Rey are sent to check out the facility, but Rey suffers a mysterious reaction as they explore the deserted Lodonia laboratory.