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.

After the previous battle, Amata and Mikono are brought to the Neo-DEAVA headquarters to evaluate their potential as Elements. Separated from Mikono and eager to meet her, Amata joins his classmate Andy W. Hole in an attempt to sneak underground into the female dorms, leading to an accident that put him on bad terms with her. Later, Amata is selected for a simulation battle, and he decides to make use of it to make amends with Mikono.

Jin assembles a new remote-controlled machine and launches it to confront Aquarion. Amata and the others are pinned down by the enemy's lasers until they are assisted by another element, Yunoha Thrul, who incorporates her invisibility powers into Aquarion Evol to allow a counterattack.

Kagura wreaks havoc at the academy while Jin takes the opportunity to hijack one of the Vectors and escape with Yunoha. Mykage appears before Fudo, demanding the location of the original Aquarion, while Kagura easily overpowers the Elements with his power that allows him to reverse the laws of physics. Jin, moved by Yunoha's tears, has a change of heart and returns to assist the others against Kagura.

Fudo still has not returned from his travel, and despite not knowing his whereabouts, Mikono leaves the academy to look for him, while Mykage appears before Zessica stating that he will open a dimensional gate to Altair, upon claiming some compensation from her in the future. A team of elements is assembled to pass through the gate and infiltrate Altair, in an attempt to rescue Mix.

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.