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.

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.

Believed to not have any elemental power at all, Mikono decides to leave the Neo-DEAVA Academy, but Kagura's comrade Jin Muso launches an attack on Vega. His tactics overpower the Aquarion Gepard, piloted by Mikono's brother Cayenne Suzushiro, that is until Neo-DEAVA's commander Zen Fudo reassumes his post and arranges for her to join the battle.

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, who was enticed by Mikono's scent, reappears determined to take her with him, but Amata flees away with her in tow. To confront Kagura, Element Schrade Elan ignores the risks to his frail health, piloting the newly formed Aquarion Spada.

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.

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.

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.

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.