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 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 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.

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.

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.