In Holy Genesis Era, in the year 0011, mankind has lost 2/3 of its population. The Great Catastrophe, which ruined the planet 11 years ago, caused the ice of Antarctica to melt.

In Atlantia, believed to have been destroyed long ago, the winged race of Shadow Angels awakens from a 12,000-year slumber. They send their bio-mechanical mythical beasts to harvest the life energy of humans, Plana, attacking the few remaining cities.

Humanity was fighting a losing battle when the Godspeed Magician Fudo Gen excavates the so-called Vectors in the sea near Crete. These three legendary machines, Mars, Luna and Sol, are now piloted by gifted youths possessing the Element to activate them, and to unite as the legendary Mechanical Angel Aquarion... but only if their heart, body, and soul can synchronize.

Source: official site, adapted by mahou (edited)

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Alternative setting: Sousei no Aquarion (2007)
Sequel: Aquarion Evol
Other: Aquarion Logos
Side story: Sousei no Aquarion Evol