This story takes place on an island named Southern Cross Isle. One night, a boy named Takuto washes up on shore, after having swum from the mainland. He later enrolls in Southern Cross High School as a senior and makes new friends. However, underneath the school, is a group of mysterious giants called Cybodies. There are about 20 Cybodies, and they are just some of the various secrets kept by everyone on the island: The secret movements of the mysterious organization known as the "Glittering Crux Brigade", the songs of the shrine maidens. Takuto himself will soon come to embrace a great secret.