It all comes down to this! As Mikage's dark Aquarion sucks up power from Altair and Vega, the future of existence lies in the hands of Amata and his fellow Elements. Will their combined powers be enough to stop the revenge-fueled angel?
Kagura and Amata's battle rages across the sky as Andy desperately tries to talk some sense into a brainwashed Mix. Meanwhile, Mikage forces Mikono into a forbidden union, and the fates of two planets hang in the balance.
Andy uses his powers to open up a hole in space while Amata's mother reveals his father's true identity. As forces from Vega and Altair clash, Fudo wonders if the revival of the legendary Aquarion will save the two worlds or destroy them both.
High Commander Fudo opens a mysterious book that unveils the secret history between Altair and Vega. Lost in a rift between dimensions, Shrade pushes his powers to the limit, and Zessica is called upon to fulfill her promise to Mikage.
Kagura's history is revealed following the life-changing revelation of his origin, and Amata finds himself in a fight against destiny. Meanwhile, the legendary Aquarion surfaces, but its arrival has dire consequences for the rest of the planet.
Amata defies orders and travels to the city where he and Mikono first met, in search of the missing girl. Several of the students from the academy follow him there, where they run into a deadly enemy, and Amata has a shocking revelation about Kagura.
Mikono tracks down High Commander Fudo and learns about the enigmatic man's past. Meanwhile, Amata discovers the truth about his mother's abduction, the curse on Altair, and the terrifying transformation that Mix has gone through.
Zessica makes a deal with Mikage to open a Dimension Gate, allowing a squad from the academy to infiltrate Altair. On the foreign planet, the students fan out and try to find Mix - but Amata stumbles across someone he has a much deeper connection with.
The leader of Altair shows up at the academy with a proposition: hand over the strongest female, or face all-out interplanetary war. In the heat of battle, one of the students makes a bold sacrifice in order to keep the rest of the Elements safe.
Several students are sent on a top-secret mission that involves digging up the legendary Aquarion, swimsuits, and…bananas?! Things take a turn for the cold, though, when an Abductor with icy powers crashes the party and spoils all the fun.
Academy administration kicks Element training up to the next level by staging a mock battle between two Aquarion units. In the middle of the fight, Zessica makes a shocking confession that sends her Aquarion formation into love overload.
Kagura, the red-haired wolf from Altair, kidnaps Mikono and reveals that he believes they are reincarnations of Apollon and Sylvie. When Amata finally catches up with the two, he realizes that he and Mikono might not be destined for each other after all.
A funeral is held for the casualties of the academy battle as the administration realizes that the people of Altair are trying to kidnap female Elements. In order to have a chance at stopping the enemy, the remaining students need to be buried...
Kagura crashes the anniversary party, turning the academy grounds into a battlefield. The school's survival depends on whether or not Jin has a change of heart about where his allegiances are - but the consequences of that choice could prove deadly.
Jin starts to get interested in coed Unions, Amata shares memories of his mother with Mikono, and the Neo-DEAVA academy celebrates the anniversary of its founding with a special screening of Skies of Aquaria.
Jin infiltrates the Neo-DEAVA academy by pretending to be a transfer student. His mission is to observe the Rare Iguras—girls—in order to find the strongest among them, but this leads to an unexpected development when he gets close to one of his subjects.
The mysterious Mikage sends rogue Abductors to avenge Jin's apparent death, even though no one in Vega or Altair is certain of his fate. Mikono's Element power is finally revealed when an odd mixture of pilots is sent out to defend the school.
Jin travels to Vega to bring a bride back to his womanless planet. His sights are set on one of the Elements from the academy, but Amata and his team show up to stop him and discover that the less they're wearing, the more heightened their senses become.
There's a strange doll floating around Neo-DEAVA, leading students to wonder if a ghost is haunting the halls. The cursed doll might be the only thing that can save Amata and his team, though, when an enemy pins them down.
When Kagura, the mysterious boy from Cayenne's prophecy, tries to kidnap Mikono, it's up to Amata and the rest of the academy Elements to keep her safe - but one of them might not make it out of this ordeal alive.
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.
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.
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.
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.
This is a retelling of the second half of season one and the plot remains virtually identical. It follows events from just after Sirius and Sylvia betray the other Elemtns through to the final confrontation with the Angels.
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