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.

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.

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.

12,000 years after the war against the Shadow Angels, Amata Sora spends his days working in a movie theater until he meets and befriends a girl his age named Mikono Suzushiro.

When a mysterious invading force, known as "Abductors" from the planet Altair and led by Kagura Demuri, attacks, Amata and Mikono find themselves in danger, until Amata activates his hidden levitation power and unlocks the sealed power of Aquarion to form Aquarion Evol.

Kagura wreaks havoc at the academy while Jin takes the opportunity to hijack one of the Vectors and escape with Yunoha. Mykage appears before Fudo, demanding the location of the original Aquarion, while Kagura easily overpowers the Elements with his power that allows him to reverse the laws of physics. Jin, moved by Yunoha's tears, has a change of heart and returns to assist the others against Kagura.

The elements mourn the deaths of Jin and the other students who perished in the previous battle. After their funeral, Fudo orders Andy to dig graves for all the remaining pilots to be buried too as part of a special training. Mikono refuses to take part on the training, but when she feels her friends' lives in danger, she helps them by activating her own element power.

The elements struggle against the Ancient AQ without success until Amata and Mikono get reunited. After confessing their feelings for each other, they form Aquarion's ultimate form, Aquarion LOVE to stop Mykage's plans and save both Vega and Altair from destruction.