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.

Fudo decides to hold a mock battle between two Aquarion despite being informed of the risks. Amata, Mikono and Zessica, all piloting Aquarion Evol, are overpowered by their opponents until Zessica confesses her love for Amata, triggering a reaction that displays the images of Apollo and Silvia along with the events regarding them 12,000 years before.

Informed that Altair is at the brink of collapse, Izumo Kamurogi, the commander of the Altean forces, finally takes into his hands the matter of obtaining the True Eve and attacks the Neo-DEAVA base by himself. The Elements little can do anything against Izumo, who demands the academy to surrender one of their female students. Zessica, heartbroken for having her feelings for Amata unrequited, volunteers herself to attend his request, until MIX tries to stop her and is captured by the enemy instead.

Amata learns from Kagura how they, who once were one and the same were separated into two different beings. While Amata and Kagura have a vicious fight in front of Mikono, the original Aquarion is unburied and Shrade pushes his life to the limit to confront an enemy machine sent by Mykage.