Two weeks have passed since the Daedalus operation. A squadron of UN bombers are sent to deal with the AI at its facility, but are destroyed by yet another typhoon. After visiting the ruins of Duomo, Kunihito brings Kuniko to witness a strange occurrence, where a star-shaped pattern appear on the ground with Atlas at the center when their blades meet. Nagiko and Talsian explain this further, revealing that the symbol first appeared when the second Great Kanto earthquake occurred. When Atlas was built on it, they are unable to stop the oscillations from happening, and used the sacrifice of young girls to Hiruko to stabilize the seismic changes. Kunihito's blade is stolen by Karin and both sun and land blades are presented to Mikuni. Karin intends to make Mikuni the successor so she will get more richer and powerful. Karin is informed by her peers that Medusa intends to destroy the world economy and create another Great Depression. Ryoko tips off the UN to Karin's presence in Akihabara and they send an aerial fortress, Titan, to wipe out the city. An explosion destroys a large part of Akihabara but Mikuni and Sayoko are protected by Miko/Hiruko, who vanishes after expending his powers.
Deux semaines après les bombardements, Kusanagi fait part à Kuniko d'une découverte qu'il a faite : des lignes formant un motif occulte sont tracées de part et d'autre des terres brûlées de Tokyo. Alors que la genèse du projet Atlas commence à se révéler, Kusanagi se fait voler sa dague sacrée...
焦土と化した東京で、國子は草薙と光の筋を見つける。
その光は東京中に走り、荒唐無稽な線を描いているかと思いきや、やがて巨大な印を結ぶ。
一方、暴走を続けるメデューサは南極大陸に向けて巨大な投資を開始。
しかし固有の領土ではない南極への巨額投資が、世界経済を破綻させるきっかけとなってしまった！
Kuniko encuentra a Kusanagi y un rayo de luz en el Tokio carbonizado. La luz recorre todo Tokio, preguntándose si traza una línea absurda y finalmente deja una gran marca. Mientras tanto, Medusa, que sigue huyendo, comienza una gran inversión en el continente antártico. Sin embargo, una gran inversión en el Polo Sur, que no es un territorio único, ha provocado el colapso de la economía mundial.
