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An attack by abductors interrupts Amata's date with a beautiful girl named Mikono. When fighters from Aquaria arrive to protect the city, Amata ends up unleashing the legendary robot Aquarion.
Amata unlocks his hidden levitation power as the Abductors from planet Altair keep attacking. Together with Mikono, he awakens the sealed power of the Aquarion and forms Aquarion Evol to fight back.
Amata and Mikono are taken to the Neo-DEAVA headquarters to be evaluated as Elements. Eager to see her again, Amata follows his classmate Andy in a plan to sneak into the girls' dorms, which goes wrong and turns Mikono against him. When a simulation battle is announced, he sees his chance to make amends.
Convinced she has no elemental power, Mikono decides to leave the academy just as Jin Muso attacks Vega. His tactics overwhelm Mikono's brother Cayenne in Aquarion Gepard, until commander Zen Fudo returns to duty and sends Mikono into battle.
The academy becomes coed, but Fudo strictly forbids the Elements from falling in love. He then sets up an unusual group activity to test how well the pilots work together.
Drawn by Mikono's scent, Kagura returns to take her away, but Amata escapes with her. To face Kagura, the frail Schrade Elan ignores the risk to his health and pilots the newly formed Aquarion Spada.
Jin launches a new remote-controlled machine against Aquarion, pinning Amata and the others down with lasers. Another Element, Yunoha Thrul, joins Aquarion Evol and uses her invisibility to turn the fight around.
Jin now fights in person and challenges Aquarion again. Zessica Wong, piloting Aquarion Spada, finds a flashy way to reveal her power and dodge his attacks, reversing the situation.
Andy and MIX cannot stop arguing, until enemies come to avenge Jin, who is believed dead. Putting their differences aside, they fight together, but MIX's takeover after Andy is hurt has backfiring results.
Jin survived the destruction of his machine and infiltrates the academy as a transfer student, searching for the "True Eve" the Alteans want. Yunoha approaches him, wanting to become his friend.
Kagura is held back by the mysterious Towano Mykage until he breaks free. His escape stirs up Altair, as he is determined to find Mikono and claim her for himself.
The students hold a screening of "Skies of Aquaria", a film inspired by events from 12,000 years earlier. Amata tells Mikono that its lead actress Alicia is his mother, who vanished when he was a child, while Jin, attached to Yunoha, decides to take her to Altair.
Kagura wreaks havoc at the academy, and Jin uses the chaos to steal a Vector and flee with Yunoha. Mykage demands the location of the original Aquarion from Fudo, while Kagura's power to reverse physics overwhelms the Elements. Moved by Yunoha's tears, Jin returns to help.
The Elements mourn Jin and the other students who died in battle. Fudo then orders a harsh special training in which the pilots are buried alive. Mikono refuses, but when she senses her friends in danger, she awakens her power of connection to save them.
After the training, Kagura finally kidnaps Mikono. Zessica, jealous of Amata's desperation, tells him that Kagura and Mikono may be the reincarnations of Apollo and Silvia, but Amata still goes to rescue her.
Fudo orders a risky mock battle between two Aquarions. Amata, Mikono and Zessica are overpowered until Zessica confesses her love for Amata, which triggers visions of Apollo and Silvia and the events of 12,000 years before.
The Elements are sent on a secret mission and wait by a lake, where they relax together. Andy tries to confess to MIX and angers her, until an enemy appears and creates a blizzard. Andy's power finally finds a hot spring that saves everyone and lets them fight back.
Altair is close to collapse, so commander Izumo Kamurogi attacks the Neo-DEAVA base to obtain the True Eve. He demands one of the female students, and Zessica, heartbroken, offers herself, but MIX steps in and is captured instead.
Fudo is still away, so Mikono leaves the academy to search for him. Mykage offers Zessica a dimensional gate to Altair in exchange for a future favor, and a team of Elements goes through it to rescue MIX.
Amata finds his mother's dormant body, and Izumo reveals that the True Eve is the only hope to break the Curse of Eve, the reason for the invasions. As the Elements flee the Altean forces, they face an enemy machine piloted by MIX herself.
