|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. That is, until one of their kind, Apolonius, fell in love with a female human warrior, Seliane. Apolonius joins forces with the humans to free them from their oppression, by using the legendary giant fighting robot Aquarion (アクエリオン Akuerion).
Eleven years prior to the story, a disaster only referred to as the "Great Catastrophe" destroyed/devastated significant parts of the world and killed off many of its inhabitants. Along with the disaster came the return of the Shadow Angels who have been in slumber in their city of Atlandia (アトランディア Atorandia) since their battle with Apolonius. The Shadow Angels began invading human cites on Earth to harvest human beings, dubbing them as "the wingless ones", like cattle, to extract the prana (プラーナ purāna, life force) from the harvested humans not only to serve as energy and nutrition to them, but also to feed the legendary Tree of Life (生命の樹 Seimei no Ki). 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). They are sentient, yet there are times when they are piloted by Shadow Angels.
Ordinary weapons prove ineffective against the Cherubim, but a human expedition under the leadership of Gen Fudou 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. The three Vectors are colored mostly in white and are shown 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). DEAVA discovers 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. 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.
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 become convinced of this when he single-handedly unites the Vectors into the Solar Aquarion formation and defeats the enemy, thus recruiting him to join their ranks.