Ayato Kamina, Hiroko Asahina, and Mamoru Torigai are on their way to a chemistry test by train with a woman who had been following Ayato. The train suddenly crashes due to an earthquake, leaving Hiroko and Mamoru injured. After leaving to find help, Ayato is distressed upon seeing Tokyo suddenly being invaded by futuristic aircraft fighters, though a giant Dolem named Allegretto has later been sent to defend the capital. In the rubble, Ayato mysteriously encounters Reika Mishima, nostalgic of her appearance. In the subway, federal agents have come to arrest Ayato, but the mysterious woman manages to save him. Ayato, after declining to go with the her, decides to board a train with Reika, reaching towards a special station called "The Shrine of Xephon" under Tokyo Bay. Once inside, they find an area covered by 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. The egg suddenly cracks, revealing wings inside.