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. An Abductor attack interrupts Amata's date with Mikono. When Aquaria fighters show up to protect the city, Amata somehow ends up unleashing the legendary mecha 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.

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

With the separation between male and female sections abolished, the Neo-DEAVA Academy becomes a co-ed institution, but Fudo declares that the elements are expressibly forbidden to fall in love with each other, and 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 and Amata flees away with her. 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 kinda flashing way 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, and they put aside their differences to confront them.

Having survived the destruction of his machine, Jin infitrates the Neo-DEAVA academy. 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 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.

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 the main actress of the film Alicia, who happens to be his mother that disappeared when he was a child. Meanwhile Jin, who grows attached to Yunoha, decides to take her with him to Altair.

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 revert the laws of physics. Jin, moved by Yunoha's tears, has a change of heart and returns to assist the others against him.

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 too as part of a special training. Mikono refuses to take part on the training, but when she feels her friends' lives in danger, she helps them by activating her own element power.

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 they may be the reincarnations of Apollo and Silvia, thus being destined to each other. Despite that, Amata confronts Kagura to rescue Mikono.

Fudo decides to hold a mock battle between two Aquarion despite being informed of the risks. Piloting Aquarion Evol, Amata, Mikono and Zessica are overpowered by their opponents until Zessica confesses her love for Amata, triggering a reaction that displays to them images of Apollo, Silvia and 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. Soon another enemy appears, creating a blizzard that covers the entire area. The elements are about to be frozen to death while a hopeless Andy sinks into a hole created by his powers until hitting a stream of hot water that helps the others to fight back.

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. The elements little can do against Izumo and he contacts the academy, demanding it to surrender one of their female students. Zessica, heartbroken for having her feelings for Amata unrequited, volunteers herself to attend his request, until Mix tries to stop her and is captured by the enemy instead.

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.

Amata discovers the dormant body of her mother and is approached by Izumo who reveals to him the reasons for Altair's attack on Vega while Andy breaks free from his imprisonment and keeps searching for Mix. Zessica and Yunoha start feeling strange and Shrade forms Aquarion Spada with them to pick up Andy and Amata. While struggling to escape from the Altean forces, the elements confront an enemy machine piloted by no other than Mix herself.

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. There, Kagura meets Amata and finally remembers the connection between them.

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 unburied 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. Labeling Mikono as their True Eve, Izumo and his forces attack Kagura determined to take her from him by force and Mykage finally claims his reward from Zessica by posessing her body.

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.

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, and 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.