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.

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.

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.

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.

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 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. 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.

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 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 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 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 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.

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. 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.

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.

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 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. Zessica and Yunoha start feeling strange and Shrade forms Aquarion Spada with them to pick up Amata and Andy. 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. 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.

Pierre Vieira and Silvia de Alisia are out on a mission in Arc City to find the reincarnation of the "Solar Wing", and their current target is an orphan named Apollo. However, Shadow Angels suddenly attack the town, and DEAVA sends out a Vector unit consisting of Sirius de Alisia, Glen Anderson and Hong Lihua to deal with the threat.

After the battle, Apollo has been put into detention until DEAVA can find out more about him. Meanwhile, Sirius, Raika and Silvia head out to battle more Shadow Angels, but trouble arises as yet another Cherubim arrives. It is revealed though, that these Angels are but mere soldiers, as this one is controlled by a human-like Shadow Angel known as Toma. What's more, Toma has a connection to Apollo's previous life...

Apollo enters the Element school, where the Elements train. The new recruits - Apollo, Jun Lee and Tsugumi Rosenmeier - then enter a training simulator, and Apollo ends up being partnered with Silvia. In the simulator, the two accidentally shares a kiss. Later on, the Shadow Angels appear yet again, and Silvia, Sirius and Raika heads out to attack them. However, Apollo accidentally winds up in Silvia's Vector, and now they need to co-operate to fight properly.

At a meeting of Shadow Angels, Toma reveals his plan of creating a new world with the help of the Solar Wing. Elsewhere, at the Element school, the Elements do an exercise which includes being barefoot. Later on, when a gravity-canceling Shadow Angel attack, their exercise proves to be very helpful.

Apollo wants to search for Baron, and goes missing trying to look for the Vectors. This leads the Commander to initiate a special exercise for the other Elements: Find Apollo. What they doesn't know is that the exercise has a special meaning, which is to work together as a team. When Shadow Angels attack later on, Apollo, Silvia and Pierre manage to learn this lesson, and they beat the Mythological Beast which has appeared.

The Elements are doing the Image Power long-range projection exercise. In this exercise, they're going to make their partner, who will be 1 000 meters away, turn around with their Image Power. However, all of them fail blatantly. Aside that, Sirius and Raika is developing a closer relationship, which makes Silvia extremely jealous.

After a small accident, tension arise between Sirius and Apollo. Later on, a Mythological Beast attacks Memphis, and Sirius, Silvia and Sirius head out to counterattack. However, it sends out a bright light which causes each of them to experience short, painful flashbacks. When they then try to unificate, they end up trying to kill each other.

Jun and Tsugumi are both worried about their first unification, and ask Pierre and Reika respectively about it. Tsugumi however, is very hesitating when it comes to going on a mission because of her powers. Later, when a new kind of Kelbim soldier appears, Jun, Apollo and Pierre are sent out to stop it; Pierre replacing a hesitating Tsugumi.

The Mythological Beast Titania has appeared, and it abducts children in their dreams, causing them to never wake up again. Most of the Elements also gets caught, but some of them wake up again, and they need to find a way to fight this Mythological Beast.

Ignoring orders, Apollo the lead and unites. The prototype wing, the new model cherubim soldier who inspired life, appears. The game wing both wings ([moroha]) you board in the cherubim soldier, the power is unfathomed. Apollo the hand or the foot does not come out in the attack whose both wings are extreme, finally [shiruvuia] owes the serious illness. It starts to beat the Sirius which runs in Apollo which created the cause of [shiruvuia] injury. .

Hong Lihua, best known as "Reika", blames herself for the event that put her and Sirius' friend Glen in a coma. Her element powers, able to bring misfortune to her and those close to her, causes her a lot of grief, until she learns to make good use of them in their following battle.

The researchers at DEAVA recover a mysterious feather dated from 12.000 years before, after learning of it, Apollo and Silvia sneak into the lab where the feather is and upon touching it, they have visions of the past involving Apollonius and his human lover Celiane.

Touma and his partner Otoha launch an attack on DEAVA together to retrieve the feather. During the battle, Apollo manages to finally reencounter Baron under Touma's mercy, just to witness his friend's death when the cage he is imprisioned explodes, much to his despair.

The Shadow Angels send an invisible enemy that proves himself more than a match for the elements. Apollo joins the fight, but he and his vector vanishes and Silvia starts realizing her feelings for him and uses them to bring him back

Element Pierre Vieira enters in a dangerous state after he learns that his former girlfriend Esperanza is about to get married, thus he is temporarily forbidden to pilot Aquarion. Soon after, the Shadow Angels launch an attack on Pierre's hometown and upon learning that his comrades are having a hard time fighting to protect it, he regains his composure and joins the fight to protect his family and friends.

The other elements are suspicious that their comrade Rena Rune is actually a vampire and once again Touma decides to take advantage of the situation in a ploy against them.

The Shadow Angels launch a special microbe that devours all of DEAVA's food supply. After a week of hunger and under enemy siege, Silvia, Tsugumi and Reika decide to fight back when they realize that not out of concern for their lives, but for their body shapes too

Fudo holds an exercise with the elements impersonating each other with hilarious consequences. Soon a enemy mimicking Aquarion's appearance and powers appears, and still under influence of the exercise, they have a hard time fighting as they used to until they finally learn to bring forth the true power of their own personalities.

The elements are drawn into a strange illusionary world and while trying to escape from it, Sirius is approached by Touma who claims he hides his true self from the others, while Apollo is confronted with his feelings over Baron's loss.

Futaba, the youngest among the Shadow Angels launch an attack on Aquarion, just to be captured by the military. The elements and the Shadow Angels hear in their minds Futaba's screams as the military scientists experiment on him, much to Touma's anger.

During Touma's next attack, he exposes to the other elements the truth about Silvia and Sirius' origins. Taking advantage of their shock over his revelation, Touma manages to convince Sirius to abandon his friends and join the Shadow Angels' side.

The elements have a hard time trying to cope with Sirius' defection, but it does not take long for him to appear before them again, now as an enemy

The elements' fight against Sirius is interrupted by the military, who despatches a new fighting machine modeled on Aquarion piloted by Glen, who recovered by having some of Futaba's feathers implanted on him. Sirius tries to convince Silvia to abandon the humans and join the Shadow Angels just like he did, but Apollo intervenes to dissuade her.

A mysterius snow covers the entire globe, turning people into plants. Silvia and Apollo have some quality time together until they are interrupted by Sirius who kidnaps Silvia. The snow starts infiltrating the DEAVA base forcing the elements to board Aquarion and fight back.

Both Aquarion and the Military manage to reach the Shadow Angels' base at Atlantis. Touma manages to restrain Aquarion and reveals the truth about the reincarnations of Apollonius and Celiane, before trying to kill both Silvia and Sirius.

Touma's plan to renew the Tree of Life using Aquarion fails. When the tree starts collapsing, the whole world starts tearing itself apart. Apollo, Sirius and Touma board Aquarion and sacrifice themselves to save the planet, but not before Apollo declares his love for Silvia, promising to reunite with her in 12.000 years.

Part 1: In a distant future there is an organization called Deava which had to fight against the so called "Shadow Angels", creatures that had survived for over

Part 2: 12,000 years whose only purpose was to destroy humanity. Apollo, a seemingly normal human, was in fact the reincarnation of a fallen Angel called Apollonius, who in turn had to fight against Touma, a Shadow Angel, along with his comrades in order to prevent the destruction of the Earth.