Over ten thousand years following the Genesis Aquarion era, humanity resides on the star Vega, constantly threatened by interdimensional invaders called Abductors from Vega's sister star, Altair. These Abductors raid Vega to steal human lives. To counter this menace, the Neo-DEAVA organization was created, deploying advanced mecha known as Aquaria, which are strictly divided by gender, with rules forbidding any interaction between males and females in both daily life and combat. However, the arrival of a powerful Abductor mecha shatters this order. In the midst of this crisis, two youths, Mikono and Amata, become drawn into the conflict. Unknown to them, Amata breaks a critical taboo by activating an Aquaria and performing the Forbidden Union, combining male and female Aquaria. This act horrifies Neo-DEAVA, with consequences far beyond Amata's understanding. Questions arise about how he can pilot an Aquaria, how he knows of the Forbidden Union, and why Mikono unexpectedly possesses the ability to operate the mecha as well.