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.

Since his last battle with Aquarion, Kagura is restrained by the mysterious Mykage Towano until he manages to break free, causing a huge commotion in Altair, as he is desperate to find Mikono and claim her for himself.

Believing that Kagura is the responsible for his parents' death, Amata launches himself against him and their confrontation opens a portal that puts Altair en route of collision with Vega. MIX regains her lost memories, thanks to Andy. After assuming full control of Zessica's body, Mykage makes use of Mikono and Kagura to take possession of the Legendary Aquarion for himself, converting it into his own mecha, the Ancient AQ.