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 anything against Izumo, who demands the academy 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.

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. As the Elements are about to be frozen to death, a hopeless Andy sinks into a hole created by his powers until hitting a stream of hot water, which then helps the others to fight back.

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.

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. Despite that, Amata confronts Kagura to rescue Mikono.

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. Mikono refuses to take part in the training, but when she feels her friends' lives in danger, she helps them by activating her own elemental power of connection.

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.

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. Meanwhile, Jin, who grows attached to Yunoha, decides to take her with him to Altair.

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.

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.

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. After Andy takes a crucial hit, MIX takes over command and defeats the enemies with backfiring results.

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.

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, 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.

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.

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.

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.

Part 2: 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.

Part 1: 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.