This is a remix, theatrical release of the first half of the Appleseed XIII series.

Years ago, humanity almost got wiped out by huge magical armored insects that had become too strong and aggressive to handle. Because of these giant bugs, humans do not live on the earth anymore, but in floating cities instead. However, this does not mean that everything is lost, because the wizards from prestigious floating wizard academies are fighting these monsters. Kanata Age is a young man now labelled as a traitor even though he was once praised as the "Black Master Swordsman." He gets a chance to repair his reputation by instructing the team E601, which seems to be facing some difficulties. It consists of three girls, Misora Whitale, Lecty Eisenach, and Rico Flamel, each with problems of their own. It appears that Kanata will get in deep waters more than once because of them...

With the initiation of the Patrian civil war came the creation of half-beast, half-human soldiers—a development of the outnumbered Northerners in a desperate attempt to counter the overwhelming Southern forces. Able to quickly dominate battlefields and achieve victory with ease, the soldiers' godlike abilities earned them the name "Incarnates." However, as the war raged on, the Incarnates encountered a problem involving the beasts inside them that they were unable to rectify by ordinary means. Once the war was over, mysteries and accounts of the Incarnates submitting to the misfortune of their war days surfaced. Aware of the horrors they faced during the war, Special Sergeant Major and former captain of the Incarnates Hank Henriette becomes a Beast Hunter—those who take the lives of Incarnates who have succumbed to the issues they experienced on the battlefields. After witnessing her father, a former Incarnate soldier, meet his end at the hands of one such Beast Hunter, Nancy Schaal Bancroft resolves to hunt the man who took her father's life. However, Nancy's eye-opening encounter with the Beast Hunter influences her to instead seek the reason behind her father's death and the Incarnates' problematic existence in society. [Written by MAL Rewrite]

Lufy, discovered floating lifeless in space, is brought on board a Solnoid cruiser and given another chance at life. Once the hardened warrior, she is shown events that shake her faith (one's own death seems to have a way of changing one's philosophy) and lessening her power as a fighter just as that power is most needed!