Since his last battle with Aquarion, Kagura is restrained by the mysterious Mykage Towano until he manages to break free, causing a huge commotion in Altair, as he is desperate to find Mikono and claim her for himself.

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 alive as part of a special training. Mikono refuses to take part in the training, but when she feels her friends' lives in danger, she helps them by activating her own elemental power of connection.

Believing that Kagura is the responsible for his parents' death, Amata launches himself against him and their confrontation opens a portal that puts Altair en route of collision with Vega. MIX regains her lost memories, thanks to Andy. After assuming full control of Zessica's body, Mykage makes use of Mikono and Kagura to take possession of the Legendary Aquarion for himself, converting it into his own mecha, the Ancient AQ.