After the event that occurred with Kagura, Sharde is seen inside a hospital, recovering his strength after piloting Aquarion. Crea enters his room to check on his condition. Sharde claims that he is able to hear the melody of Aquarion. He states that if he listened to it longer, he could grasp its full melody, to which Crea tells him not to push himself too hard. Because Sharde insists that he must hear it, Crea gives him a waiver that allows him to ride Aquarion whenever he pleases.
Back at school, Andy tells the class that although the school is co-ed, the walls in their hearts are still blocking them from any further relationship. Andy proposes that they should have a new seating arrangement so that the boys and girls can mix seats and grow closer to one another. While Mix is against such an idea, the remainder of the class is interested and tries it out. The seats are randomly generated, and the student take turns finding a seat via lottery. Zessica sits next to Amata, who sat across from Mikono. Cayenne and Sharde, who were not in class were placed next to each other with Sazanka sitting behind them. Despite Andy’s goal to be surrounded by girls, he ends up sitting across from Mix and next to a doll. Andy is curious about the doll and why it was there. Andy tells some classmates about the story of a girl years ago who had the exact same doll as the one in class. The girl was shy and had a hard time making friends. When she could not stand the loneliness anymore, she vanished from the world, leaving her doll behind. At night, one could see the doll moving around and singing to its holder. Zessica claims that his story is ridiculous, but Malloy heard a similar story as well. Andy tries to scare the class once more, but it overall fails.
Later that night, Amata was in charge in cleaning the school. When he was finished, he was about to leave until he spots Zessica at the door. Zessica states that since the two are together and leaving, they should walk out together. Apparently, the door out of their school was locked. Since their dorms are in opposite ends, Amata decides to head out from the boy’s side, but Zessica insists that he gets out from the girl’s side with her. As they were walking towards the exit, Zessica clings onto him tightly. Amata asks if she’s scared, to which she lets go, claiming that she is not scared of the story Andy told them earlier today. However, the same doll was found not too far away from them, and a voice other than their own can be heard. The doll floats up and moves towards them. Amata and Zessica were easily scared with Amata flying and Zessica pushing him with her out of the school. Meanwhile, Mikono was walking outside, still wondering about who Kagura was and what he meant to her. She then sees Zessica running away with Amata in full speed. Mikono easily misunderstood what was going on.
At the enemy base, Jin was practicing ways to defeat Aquarion. Izumo tells him that, despite defeating Aquarion every time, she simulations are meant to help gear him for a real fight. Jin wishes to go back to that world once more, to which Izumo gives him permission to. Jin flies out and goes to a wormhole. Kagura, trapped in a cage, yells at Jin to come back and not do anything to Mikono.
The next day, Amata and Zessica tell their classmates about what they saw. Andy states that what he said was a joke and nothing to take seriously, but they were hell bent to believing in what they saw. Mix, on the other hand, asks why the two were in school at night to begin with. Before Amata could say anything, Zessica covers his mouth, telling him not to say anything about last night. Because they were silent, Miz assumes that they did something dirty at the school grounds. Mikono complicates the situation, telling from her point of view what she saw between Zessica and Amata. Amata tries to tell Mikono that she got it all wrong, but she would not listen.
An emergency call appears, stating that abductors have been found in the city. Zessica, Amata, and Cayenne were sent to fight against the abductor. As soon as they fly away, the enemy quickly fires its laser gun at them from a long distance. Dante tells them to form a Union quickly since it might be dangerous for them to fight via Aquarius. Zessica calls out Aquarion, and Aquarion Gepard is created. Gepard continues to close in on the enemy using the buildings as cover, but Jin already knew something like that would happen. Jin releases many metal spheres from his machine, surrounding the area they were in. Using the spheres like a mirror, Jin fires several laser beams that shoot at Gepard in all directions. Gepard was easily pinned to the ground and was at a pinch. Amata was unable to hold on for much longer, and the Union breaks, separating them to three. Zessica blames herself for her inability to protect Amata.
Back at the school, Zen tells Mikono about the human heart and how people can easily misunderstand things. Zen proves the hidden message of his words by switching Zessica with Yunoha, the invisible girl carrying the doll. Yunoha tells Amata and Zessica that she is sorry for scaring them. She also asks Mikono to forgive them and trust her. Yunoha asks Amata to form a Union with her, to which he agrees to. Amata calls out Aquarion, and Aquarion Evol is formed. From the transformation, Yunoha’s true body is revealed. Yunoha easily gets shy from her revelation and turns herself invisible. This causes Aquarion to turn invisible as well, making Jin’s laser beams pass through it. Using her power to their advantage, Aquarion closes in on Jin’s machine. Jin starts to get desperate and fires his laser beams once more, but all proved ineffective. Jin sees that while it is invisible to light, it is still materially there. Jin fires rockets from his machine at Aquarion and hopes it works. Aquarion jumps and starts to hammer away at Jin’s machine. With one final punch, Jin’s machine is destroyed; however, Jin himself was not gone, as he was controlling his machine from the enemy base.
Amata, Cayenne, and Yunoha return to school. Mikono tells Amata she is sorry for jumping to conclusions. Yunoha, still invisible, appears before them, which makes Zessica scared. Amata introduces Yunoha to everyone, but the story Andy made up remained on his mind. Donar and Suomi has to remind him that she is a student from their school and alive, just like him. Yunoha reveals herself to everyone. Because Amata was caught off guard by her cuteness, he levitates for no reason again. While Mikono and Zessica sighed, Yunoha was quite relieved.