When Durandal assigns Athrun and Shinn to the latest ZAFT mobile suits, Shinn takes his offer with enthusiasm, while Athrun begins to doubt his role in ZAFT and ends up being branded a traitor. The Minerva sets off in pursuit of the Archangel after Durandal determines that their inability to control them renders them a dangerous foe, and during their engagement, the Archangel is seemingly destroyed, while Shinn bests Kira in combat.
In the aftermath of Berlin, the Archangel also capture Neo Roanoke and are shocked to learn he’s actually Mu La Flaga, although Mu has no recollections of anyone. Stella succumbs to her wounds, and Durandal comes forward, identifying LOGOS as the culprits behind the latest atrocities and declaring war on them. However, Shinn is shocked to learn Stella is piloting the Destroy, and although he tries to talk her down, Stella ends up panicking when she spots the Freedom, forcing Kira to annihilate the Destroy. To stop the Destroy, Kira sorties, while Shinn does the same. For their actions, both Shinn and Rey are detained, but Chairman Durandal orders the charges dropped after the Alliance deploys their new mobile armour, the Destroy, and annihilates three European cities for harbouring people supporting ZAFT, including Berlin. Rey ends up helping Shinn, who implores her handler, Neo Roanoke, not to send her into combat. When Shin learns that Stella is dying, he decides to return her to the Alliance against orders. The Archangel intervenes, and Kira manages to destroy Athrun’s Saviour, while Shinn eliminates one of the stolen Gundams. En route to Crete, the Minervan comes under fire from the amassed Earth Alliance and Orb forces.
Meanwhile, Miriallia reunites with the Archangel and takes up her old post.
Shinn brings Stella on board the Minerva for medical treatment, and the Minerva heads towards a ZAFT medical installation at Crete, while Lacus and Andrew Waldfelt head back to space by commandeering a transport meant for Meer. “No matter how many times people blow away the flowers, we’ll always plant them back.