

During the Elements' first sortie against the Cherubim by uniting the Vectors into a formation of Aquarion, they stumble on 13-year-old Apollo, who seems to be the reincarnation of Apollonius. They also discover the Elements can ultimately unite the vectors into one of three formations of the giant robot in battle, and can use it to fight and defeat the Cherubim. DEAVA discovers that only people with special powers called Elements ( エレメント, Eremento) can control the Vectors and the three vectors are in fact the pieces of Aquarion, the same robot used to fight the Shadow Angels twelve millennia before. The three Vectors are shown to be colored mostly in white and are identified as the green Vector Luna ( ベクタールナ, Bekutā Runa), the blue Vector Mars ( ベクターマーズ, Bekutā Māzu), and the red Vector Sol ( ベクターソル, Bekutā Soru).
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However a human expedition under the leadership of eventually excavates three very technologically advanced fighter planes, and an organization called DEAVA ( ディーバ, Dība, Division of EArth Vitalization Advancement) takes over the research of these machines, called Vectors ( ベクター, Bekutā), trying to identify how to use them. Ordinary weapons prove ineffective against the Cherubim, with limited protection coming only from rings of projectors built around the remaining cities which tap into the Earth's strata to project a quantum shield which limits the Shadow Angels ability to enter or materialise within. They are sentient machines, yet there are times when they are piloted by Shadow Angels. The Shadow Angels facilitate their harvesting via giant, floating harvesting machines called harvest beasts ( 収穫獣, shūkakujū) which are guarded by giant mecha called Cherubim Soldiers ( ケルビム兵, Kerubimu Hei). The Shadow Angels began invading human cites on Earth to harvest human beings, dubbing them 'the wingless ones', like cattle, in order to extract the ( プラーナ, purāna, life force) from the captured humans to serve as energy and nutrition not only to the Shadow Angels, but also to the legendary ( 生命の樹, Seimei no Ki).

Along with the disaster came the return of the Shadow Angels who have been in slumber in their city of Atlantia ( アトランディア, Atorandia) since their battle with Apolonius. Eleven years prior to the story, in a disaster referred to as the 'Great Catastrophe' the Earth's magnetic field shifted devastating significant parts of the world and killing off many of its inhabitants.

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Apollonius joins forces with the humans to free mankind from oppression, by using the legendary giant fighting robot Aquarion ( アクエリオン, Akuerion). That is, until one of their kind, Apollonius, fell in love with a female human warrior, Seliane. Further information: Twelve thousand years in the past, mankind was at mercy of the mythical creatures known as Shadow Angels ( 堕天翅, Datenshi), immortal winged beings with overwhelming powers and technology.
