When the Shadow Angels invade after 12,000 years of slumber, humanity is held captive by fear and sheer alien dominance. Eleven years after the Great Catastrophe decimated the world, most of those left alive are scavengers, dirty and starving in the streets. There is hope, however – Mechanical Angel Aquarion: Three sleek war ships flown by touched souls known as Elements. Through the perfect joining of hearts, bodies and souls, the sum of the formidable parts can be unstoppable. One feral young man, Apollo, could be the prophesized missing piece that finally completes Aquarion. Ultimate strength through unity…

The enemy rises from slumber, only to learn that his greatest foe has been resurrected, the Solar Wing. Across the galaxy, Aquarion defends humanity from the merciless alien harvest. The Elements lose their edge and their souls unravel, opening the door to their own destruction. As Apollo joins the fight, so too does an interloper from across the stars. The light that comes from darkness, the light that created the universe is released by a voice from the ages. Aquarion is torn asunder, unified force ripped apart. When the smoke clears, a new era begins.

The new class of Element recruits report for duty and Apollo is among them, making some of the more experienced pilots touchy. Apollo only wants access to Aquarion to save his best friend, but before he can take the controls again he'll need a lesson in partnership and trust. The simulation training is rigid… But simulation and reality are two different things. When an alien harvesting team appears in the city, veteran and rookie alike are pushed to the limits. What at first is a grand victory can quickly transform into tragedy. Progress is made, but it's too soon for celebration.

Within his wild heart, Apollo feels the harsh separation from his best friend Baron, who has been harvested by the Shadow Angels. The winged aliens convene and one known as Toma announces his holy dream – A vision that foretells the Earth's resurrection as a thing of beauty by utilizing the heralded Solar Wing. Back on the ruined planet, the recruits undergo a strange training exercise at the will of Gen Fudo, their new commander. Paying attention to the odd lesson might mean surviving or perishing. Another Aquarion sortie allows the pilots a chance to turn practice into practical strategy. Lessons are taught for a reason.

Apollo is lurking around the base looking for the Vectors and the commander has turned his AWOL status into a training exercise for the other recruits: Find Apollo! It won’t be as easy as it sounds to track this boy through the pits and mazes of the grounds; traps are plentiful and the prey is wily. His motivations for vanishing are personal, and his vendetta puts the whole team at risk. While humans are plucked from their beds as they sleep, new heroes vow to end the madness and bring the victims back to Earth. The goal is set, the target is Atlandia.

The Elements continue with their training, faced with new and ever more difficult challenges. In order to truly be effective against the Shadow Angels, they must learn to harness their emotions, to attack without reservation. Apollo and the other recruits begin work on their telekinetic abilities, enhancing the powers of their imaginations and spirits. When perfected, these new techniques bind partners closer, an intimate connection easily transferred into fighting strategy. The fighters will have to overcome space and time, unchanging and mysterious both like the moon above, if they wish to defeat a treacherous foe.