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.

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.