12,000 years after the events of Sousei no Aquarion, mankind is threatened by a new enemy from another dimension labeled "Abductors," who, just like the Shadow Angels, invade human cities to kidnap their inhabitants. To defend humanity from this invasion, the Neo-DEAVA organization establishes two teams, one composed of only males and the other of only females, each piloting their own giant machines called "Aquaria." To protect his new friend Mikono, teenager Amata Sora decides to use the powers he has kept secret his entire life, and by combining Vectors with male and female pilots into one single robot, the legendary giant Aquarion is reborn once more.