An Abductor attack interrupts Amata's date with a beautiful girl named Mikono. When Aquaria fighters show up to protect the city, Amata somehow ends up unleashing the legendary mech Aquarion.
Amata's secret power is revealed while piloting Aquarion, resulting in a devastating attack that sends his enemy flying. Meanwhile, Cayenne's powers of prophecy go into overdrive, and a foreboding vision of Mikono's future is broadcast for all to see.
Amata wakes up at the Neo-DEAVA academy where Element pilots are trained. The staff has all kinds of tests set up for him, but the real fun begins when he falls down a hole and helps a new friend tunnel under the wall separating the boys from the girls.
Several students are sent out to deal with an Abductor attack, only to find themselves completely surrounded. Despite not having any Element powers, Mikono might be the only person who can save them--or so says the mysterious academy groundskeeper.
The Neo-DEAVA academy goes coed and the Chairman arrives to shed light on some of the mysteries of Aquarion. When the students get broken into threesomes and assigned to participate in date-like activities, the results are shocking.
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.
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.
Now piloting in person, Jin challenges Aquarion once more, but faces another reversal when Zessica Wong, piloting Aquarion Spada, finds a way to expose her abilities in a flashy manner to avoid his attacks.
Andy and his classmate MIX are unable to understand each other and are usually arguing, until some enemies appear to avenge Jin, who is believed to be dead. Andy and MIX put aside their differences to confront the enemies.
Having survived the destruction of his machine, Jin infiltrates the Neo-DEAVA Academy posing as a transfer student. While searching for info about its female residents, he looks to find out if the "True Eve" the Alteans are desperately looking for is among them, until he is approached by Yunoha, who wants to befriend him.
Since his last battle with Aquarion, Kagura is restrained by the mysterious Towano Mykage until he manages to break free. This causes a huge commotion in Altair, as Kagura is desperate to find Mikono and claim her for himself.
The students organize a special meeting featuring a screening of "Skies of Aquaria", a feature film based on the events of 12,000 years before. Amata reveals to Mikono his connection with Alicia, the main actress of the film, who happens to be his mother that disappeared when he was a child.
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.
The Elements mourn the deaths of Jin and the other students who perished in the previous battle. After their funeral, Fudo orders Andy to dig graves for all the remaining pilots to be buried alive as part of a special training.
After the graveyard training is complete, Kagura appears before the other Elements and finally manages to kidnap Mikono. While searching for them, Zessica grows jealous of Amata's desperation to find Mikono and confesses to him that Kagura and Mikono may be the reincarnations of Apollo and Silvia, thus being destined to each other.
Fudo decides to hold a mock battle between two Aquarion despite being informed of the risks. Amata, Mikono and Zessica, all piloting Aquarion Evol, are overpowered by their opponents until Zessica confesses her love for Amata, triggering a reaction that displays the images of Apollo and Silvia along with the events regarding them 12,000 years before.
The Elements are summoned by Fudo to take part into a secret mission. Ordered to stand by beside a lake while awaiting further instructions, they decide to have some fun together. Andy tries to make use of the situation to confess his feelings for MIX, just to unwillingly bring forth her fury on him.
Informed that Altair is at the brink of collapse, Izumo Kamurogi, the commander of the Altean forces, finally takes into his hands the matter of obtaining the True Eve and attacks the Neo-DEAVA base by himself.
It have been a week and Fudo still has not returned from his travel, and despite not knowing his whereabouts, Mikono leaves the academy to look for him. Meanwhile, Mykage appears before Zessica stating that he will open a dimensional gate to Altair, upon claiming some compensation from her in the future.
Amata discovers the dormant body of her mother and is approached by Izumo, who reveals to him that the True Eve is the only hope of survival to reverse the Curse of Eve, being the reason behind the Altean invasions on Vega. Andy breaks free from his imprisonment and keeps searching for MIX.
Amata's team returns from Altair after failing to save MIX and Shrade's condition gets worse, while Mikono and Fudo keep traveling together in search of the Legendary Aquarion. After having a nightmare involving Mikono, Amata flees to the town where he first met her and he finds the place deserted.
Amata learns from Kagura how they, who once were one and the same were separated into two different beings. While Amata and Kagura have a vicious fight in front of Mikono, the original Aquarion is unburried and Shrade pushes his life to the limit to confront an enemy machine sent by Mykage.
Fudo assembles the remaining Elements and reveals to them all the truth regarding the events from the last 24,000 years and its connection with the present situation. Meanwhile, with his last ounce of strength, Schrade uses his powers to allow Zessica and Amata to cross safely to Altair.
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.
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.
The Elements, both living and dead, 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.
It was screened at Project Aquarion's 10th Anniversary event held on June 28, 2015.
