Ayato, Hiroko and Mamoru are on their way to a chemistry test with a stalker on their tail. Tokyo is suddenly invaded by futuristic fighters, and giant Dolem defend the capital. In the rubble Ayato encounters Reika Mishima. Ayato is arrested, but he's freed by his stalker; Ayato runs away from her with Reika. Ayato and Reika get on the subway and reach a special station called "The Shrine of Xephon" under Tokyo Bay. There, they discover a Dolem in storage, and further in they find a room with a blue sky, and a giant egg resting in a pool of water. The Dolems singing above affect Ayato, but Reika breaks through them with a song of her own. Suddenly the egg cracks, revealing wings inside, and Ayato says "Rah...Xephon".