Otori Sakko is a second-year student at Enoshima Academy, a private school for gifted students. Cocky and fearless, he is often shunned by his peers. One day, Sakko's recently deceased friend Sayo reappears and starts talking about 12,000 year-old myths.

The Elementals learn that the beast they fought is a Shadow Angel from mythic space. Their role is to fuse the Vector Machines into Aquarion and fight those enemies back. Sakko recalls playing with Sayo, Momohime, and a certain robot in an Enoshima cave.

The universe's ability to self-correct made Sayo's funeral occur before her death. It seems only the Elements are aware that Sayo was in their class, but when Momohime asks about it, the students share a vision of a super-civilization with winged beings.