12,000 years after the war against the Shadow Angels, Amata Sora spends his days working in a movie theater until he meets and befriends a girl his age named Mikono Suzushiro.

When a mysterious invading force, known as "Abductors" from the planet Altair and led by Kagura Demuri, attacks, Amata and Mikono find themselves in danger, until Amata activates his hidden levitation power and unlocks the sealed power of Aquarion to form Aquarion Evol.

With the separation between the male and female sections abolished, the Neo-DEAVA Academy becomes a coed institution, but Fudo declares that the Elements are expressibly forbidden to fall in love with each other. He later organizes an uncommon group activity to measure the compatibility between the pilots.

Kagura boards the Legendary Aquarion to protect Mikono from Izumo's forces. Andy manages to open a dimensional hole to Altair with his power, and upon arriving there, he confronts Mix, trying to make her return to her former self. Meanwhile, Alicia finally awakens and reveals to Amata the truth about his father and the reason why she left him behind when he was a child.

The elements struggle against the Ancient AQ without success until Amata and Mikono get reunited. After confessing their feelings for each other, they form Aquarion's ultimate form, Aquarion LOVE to stop Mykage's plans and save both Vega and Altair from destruction.