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! A rare breed of pilot takes the controls, powered by three souls intertwined. 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!

12,000 years have passed in this world, the story of Apollon and Sylvie have become a children's story called "Skies of Aquaria". The "Abductors" Invaders from Altea come to Earth with only one purpose: they invade to harvest humans. DEAVA the Aquaria Academy exists to train men and women to use Aquaria, but they cannot ever merge because of Guize stones, these block an "unholy union" between genders. The story follows Amata and Mikono in their enrollment into DEAVA, and fight the Abductors.

Once upon a time, human voices had defined the true nature of all things, yet the invention of text changed the status quo, while creating a "Logos World" between the voice and the truth. Millennia have passed since then, advancements of civilizations have made the "Logos World" too big to control "texts." A group of young people dedicate themselves to counter chaotic "texts" with "Creative Voice Power," and among them, a boy named Akira Kaibuki living in Asagaya.