創聖紀００１１年の地球－－人類はその人口の２／３を失っていた。１１年前の大異変が原因である。南極の氷が溶解し、１万２千年前に滅びたはずのアトランディアが出現、翼をもつ“堕天翅族”が蘇った。一方、人類は反撃を期して伝説の兵器であるハイブリット戦闘機“ベクターマシン”を発掘した。ベクターマシンが合体することにより、“機械天使アクエリオン”が姿を現す。
12,000 years after the events in Genesis Aquarion, humans live on the star Vega under constant threat of trans-dimensional beings called Abductors. These enemies originate from Vega’s sister star Altair and raid Vega for human life. As a countermeasure, an organization known as Neo-DEAVA formed to combat the Abductors. They pilot advanced mecha suits called Aquaria and are strictly separated by gender. Boys and girls are not allowed contact; they are even restrained from fighting on the same battlefield. However, events take a shocking turn when an advanced Abductor mecha suit joins the fray. Two teenagers, Mikono and Amata, are dragged into the conflict. Unknowingly, Amata performs a taboo when he summons an Aquaria and initializes what is called the Forbidden Union between male and female Aquaria. Neo-DEAVA is shocked, and the repercussions of Amata’s actions are much farther reaching than he realizes.
For thousands of years after its development, mankind used the written word for communication between people and generations. As millenia passed and technology became more prevalent, writing - and thus, communication as a whole - diminished, until it could only be found on cell phones and computer screens. Seeing an opportunity, the sorcerer Sogan Kenzaki starts infecting words with the Nesta Virus, which brings them to life and turns them into monsters called MJBK (Menace of Japanese with Biological Kinetic energy). To counter this attack against humanity, an organization known as DEAVA (Division of EArth Verbalism Ability) assembles a group of youths with the ability of "Verbalism". They have to pilot the vector machines, which are used to form the mechas dubbed "Aquarions". The one wild card in the situation is the self-dubbed "savior", a young man who is the direct relative of a famous calligrapher, named Akira Kaibuki.
「思い出して、翅があったころのことを」1万2千年前の想いに応え、繋がったのは欠けたこころ。太陽と月と火星が出会うとき、新たな合体の調べが流れる――！湘南の海に浮かぶ小島、江の島。美しくのどかなその浜辺に、〈私立江ノ島学園〉はある。学園には、全国から優秀な子どもが集められ、最新の機器を使った英才教育が施されていた。特殊強化クラスの生徒〈エレメント〉に選ばれたサッコ、リミヤ、トシは、感情の力で動く戦闘機〈ベクターマシン〉の操縦を命じられ、謎の侵略兵器〈神話獣〉との戦いを余儀なくされる。戦いのさなか、不可思議なヴィジョンに導かれ、サッコは叫ぶ――。「想星合体！GO、アクエリオン！」繰り返される輪廻の果てに、現れた機械天翅アクエリオン。 宿命を背負った少年少女は、得体のしれない団体〈宇宙たまごの会〉や大人たちの思惑が交錯する中、この宇宙の真実と向き合っていくことになる……。これは、おのれの感情と宇宙の存亡を賭けて紡がれる、壮大な愛の神話。
