In a distant future, humanity once again is facing the threat of the "Shadow Angels". Mystical creatures who 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 around 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 as the reincarnation of Apolonius, a fallen angel who fought against his own kind to protect mankind. Few believe it could be true, but the fact is that despite his untamed and reckless nature, he proved to be an invaluable asset in the battle against the Shadow Angels.
创圣纪0011年的地球,由于11年前的大异变,人类丧失了2/3的人口。南极冰山溶化1万2千年前灭亡的亚特兰帝亚重现于世,拥有双翼的『堕天翅族』苏醒了。他们生物机械兵器『神话兽』接连送入人类的都市,捕获人类。摄取身体能源另一方面,人类决心反击,从海底以及发掘出三台组合(hybrid)战斗机。这是1万2千年前,将堕天翅族比如灭亡绝境的传说中的兵器。Vector Machine经过合体,『机械天使Aquarion』即将现身。要启动Aquarion,需要能与体的机械生命感应和共鸣,称为『Element』的人。而后,『机械天使Aquarion』合体的时刻终于来到......