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. When a Shadow Angel stronger than the others, known as a Cherubim, appear, can they hope to win? Also, how does Apollo relate to all this?

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. Can they overcome this negative energy and win?

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. However, when it seems that only her powers can save the day, will she build up the strength to do so?

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.

The Shadow Angels unleash a dreadful new weapon, designed to be guided by their most powerful warrior. Elements are seriously injured and must heal while the Vectors are repaired in the field.

A crisis of confidence has shaken Reika to the core, forcing the depressed pilot to leave the program and her partners behind.

An artifact from a holy scripture unleashes a flood of recollection, igniting the souls of Apollo and Silvia. Toma himself visits the Earth in a war machine - and Apollo is in the crosshairs.

Apollo may be a beast, but Toma knows his weakness: the loyalty that will allow the Shadow Angel access to the relic.

The Shadow Angels are depending on the Solar Wing to deliver them unto a new world - but who is the true Solar Wing? Silvia struggles to make sense of past lives and present frustrations.

Pierre has grown addicted to merging, and there's a real chance his mind will slip into madness if he ever does it again. When the Shadow Angels attack his hometown, Pierre must choose his fate.

The recruits grow uneasy when one among them is suspected of being a vampire. As rumors float through the base, mysterious sicknesses and strange encounters within the team have Silvia intrigued.

The Shadow Angels are disgusted by the gluttonous dreams of humanity. Exploiting the ultimate weakness as punishment, the Earth's food supply begins to vanish and the populace is soon starving.

To become intimately familiar with their partners, the Aquarion recruits are commanded to dress and act like their counterparts. Some will have their feelings hurt before the lessons of the exercise become clear.

As the pilots wander in a strange land of twisted dreams, Aquarion lays broken - and Apollo and the others struggle to stay sane.

A young Shadow Angel is captured and the creature is poked and prodded in a cold laboratory. The horrible result of the torture leaves two species boiling in anger.

The Shadow Angels lust for revenge after the loss of one of their own. The line between good and evil begins to blur as secrets are revealed and bonds tested.

Ex-comrades meet on the battlegrounds of a new war. Element will fight Element, the dead will rise to fight their own, and the true Solar Wing will be revealed!

A next generation Aquarion appears and joins the fight, piloted by a victim of the unending war. As tradition and dreams clash, one girl takes a stand.

The Shadow Angels have gained the upper hand now that Sirius has joined them. Apollo must open the gates to Heaven and undertake a dangerous rescue mission - though it may already be too late.

The remaining members of the Aquarion team have broken through to Atlandia! Sirius and Apollo meet in combat, heading toward their final destiny.

The secrets of the Solar Wing have been revealed, and Aquarion may be forced to make the final sacrifice in order to save the souls of every sentient being.