The story begins in the year 11 of the Genesis century, on Earth, when humans lost two-thirds of its population due to a great disaster 11 years prior. Along with the disaster, Antarctica's ice melts and Atlandia, which was believed to have died out, appears, and the "Shadow Angels", who have wings, arise. In order to ingest life energy called "Prana", they capture many humans by launching a lot of biological-mechanical weapons, one after another.

At the same time, humans excavate three hybrid combat machines called the "Vector Machines" from the ancient seabed ruins in order to retaliate. The Vector Machines are legendary weapons that are believed to have annihilated the Shadow Angels 12,000 years ago. By the Vector Machines combining together, the "Mecha Angel Aquarion" is formed.

In order to move the "Aquarion", humans called the "Element" are necessary. The Element can sympathize and identify with the mecha's machine life. As it requires very keen five senses and ingenuous spirit, middle-teenage boys and girls are gathered as pilots.

Now, finally the time comes when the Mecha Angel Aquarion units arrive!