Ep. 1: Ayato and Reika journey to the Shrine of Xephon beneath Tokyo Bay after a train crash.

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Ayato Kamina, Hiroko Asahina, and Mamoru Torigai travel by train for a chemistry test while being followed by a mysterious woman. An earthquake causes the train to crash, injuring Hiroko and Mamoru. Ayato seeks help but discovers Tokyo is under attack by futuristic aircraft. A giant Dolem named Allegretto is deployed to defend the capital. Amidst the rubble, Ayato meets Reika Mishima, whose appearance evokes nostalgia. Federal agents attempt to arrest Ayato in the subway, but the mysterious woman rescues him. Ayato declines her offer and boards a train with Reika to reach the special station known as "The Shrine of Xephon" under Tokyo Bay. Inside, they find a sky-blue area with a giant egg in water. Dolems sing above, affecting Ayato, but Reika counters with her own song. The egg cracks, revealing wings within.