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...

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. .

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.

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.

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.