In a distant future, humanity is once again facing the threat of the "Shadow Angels," mystical creatures who have returned after 12,000 years of absence. They attack human cities and kidnap their inhabitants in order to drain their "prana" (vital energy). To fight against them, youngsters with special powers from arround the world were gathered and trained to pilot the "vector machines," three ancient ships that together form mankind's ultimate weapon, "Aquarion." The story revolves mainly around Apollo, a teenager rumored to be the reincarnation of Apolonius, a fallen angel who fought against his own kind to protect mankind.

Twelve thousand years after Genesis of Aquarion on the planet Vega, Amata Sora meets Mikono Suzushiro. Together, part of the organization Neo-DEAVA, they must defend their planet from relentless invaders attacking from Altair, a sister planet devoid of females. These two unexpected heroes, along with other young men and women, known as Elements, pilot massive robots called Aquaria, in defense of their planet, in a battle against malicious assailants trying to abduct woman from their home planet. 
(Source: One Peace Books)
 
Note: Includes 2 extra chapters.

When the Shadow Angels invade after 12,000 years of slumber, humanity is held captive by fear and sheer alien dominance. Eleven years after the Great Catastrophe decimated the world, most of those left alive are scavengers, dirty and starving in the streets. There is hope, however: Mechanical Angel Aquarion! 
 
Powered by three souls intertwined, a rare breed of pilot takes the controls. Known as Elements, one among them must rise if mankind is to survive. Prophecy is being fulfilled as the end of the world approaches... Through a swirling cloud of love, betrayal, loss and destiny, the last hope for the new century arrives and takes flight! 
 
(Source: Funimation)

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