The excessive use of the dimensional gate has caused Altair’s energy supplies to dwindle. Feeling that Altair is at the end of its rope, Izumo decides that he, himself, will head to Vega this time to bring back Rare Iguras.

Mix has been taken to Altair. While Andy is feeling down for not being able to do anything as the dimensional gate is closed, Zessica is also suffering a guilty conscious for what happened to Mix. Then, Mykage suddenly shows up in her dorm room.

12,000 years after the battles fought by Aquarion, machines from another dimension called Abductors begin attacking the Earth and kidnapping people. Two Aquarias protect humanity from the Abductors, but then a more powerful enemy appears...

Although both Amata and Mikono are brought to the St. Angel Academy in Neo-DEAVA, they’re on different sides of the Berlin Wall and cannot see each other. So Amata decides to work with Andy in order to be able to see Mikono again.

While the Element candidates are prohibited from being in a romantic relationship, they are divided into mixed-gender, three-person groups in their field trip. This activity is part of their training, but what is the purpose of this strange arrangement?

Still feeling the barrier between the guys and girls even after the academy became co-ed, Andy suggests changing the seating arrangements in the classroom. When he didn’t get the arrangements he hoped, he starts talking about an Element who disappeared.

Andy says that holes are his very life. Mix states that she hates holes. In training, they’re required to merge but refuse to do so. Despite the fact that their Gattai didn’t go well during training, Fudo sends them in to a real battle.

As Jin continues his infiltration of Neo-DEAVA, on Altair, Kagura’s rage over being held captive continues to grow as he pines for Mikono. Mykage encourages his rage until it boils over, and he breaks free in order to attempt to head to Vega again.

Just when the students at St. Angel Academy have completed their Grave Training, Kagura, who was sent to Vega by Mykage, shows up before them. Realizing that Kagura is after Mikono, the students try to help her escape.

While mourning the lost lives, students at the academy begin to realize that they’re fighting a life-or-death battle. In order to face the battle against Altair, which is expected to further intensify, Fudo assigns the students a new training.

A dark Aquarion controlled by Mykage has appeared in front of Amata and the others. In order to stop the two planets and all life from being destroyed, Amata and the others must defeat the dark version of Solar Wing.

After finding out that Amata was unable to tell Mikono how he feels about her, Andy offers his help, suggesting a get together among friends and making plans to hold an exciting event to celebrate the St. Angel Academy’s foundation day.

After his parents die as a result of Kagura’s attack, Amata becomes furious at Kagura, his other half, and attacks him using an incomplete form of Aquarion. Meanwhile, Andy continues to try hard to get Mix’s memory back.

Jin contacts Altair to let them know he is still alive. Izumo orders him to infiltrate Neo-DEAVA to search for a Rare Igler who can be the true Eve and also to attempt to retrieve all or part of the Mechanical Angel.

The Mythic Aquarion finally awakens in response to Kagura’s call. Boarding the Mythic Aquarion along with Mikono and Zessica, Kagura pilots the Mythic Aquarion and fights Izumo and Mix in order to keep them from taking Mikono away from him.

While digging a hole, Andy finds an ancient book and thinks that it is the legendary book called “The Book of the Twin Stars.” In the meantime, Jin gets on board the heavily armored Radius Gnis in order to mount another attack on Vega.