Having resolved the crisis in the Petrification Kingdom, Senkuu and his companions gear up to deal directly with the mastermind behind the petrification phenomenon—who supposedly resides on the moon. The ambitious spaceship project, however, requires immense manpower and critical resources scattered across the world. Thus, the Kingdom of Science exploration team kick-starts its transcontinental journey on the ship Perseus to gather them all. Equipped with modern technology and bolstered by the new, capable members in their ranks, the exploration team feels confident about setting sail to their first destination: America. They soon realize that the region now hosts adversaries controlling the resources they need, doing so with scientific technology which rivals and even exceeds their own. In a battle of science versus science, Senkuu and his team must outsmart their rivals if they are to have any chance of ensuring the continued survival and rejuvenation of humanity.

"Remember, when you had wings." In response to a wish from 12,000 years ago, a broken heart connects. When the sun, moon, and Mars meet, a new melody of fusion flows! Enoshima is a small island floating in the Shonan Sea. On its beautiful and tranquil beach, there is the "Private Enoshima Academy." The school gathers talented children from all over the country, and provides them with a gifted education using the latest equipment. Sakko, Rimiya, and Toshi, who have been selected as students in the special reinforcement class "Elements," are ordered to pilot the "Vector Machine," a fighter plane powered by the power of emotion, and are forced to fight against the mysterious invasion weapon "Mythical Beasts." In the middle of the battle, guided by a mysterious vision, Sakko shouts out... "Planetary Fusion! Go, Aquarion!" At the end of repeated reincarnation, the mechanical heavenly wing Aquarion appears. The boys and girls, burdened with their destinies, will come face to face with the truth of the universe as the mysterious organization Space Egg Society and the intentions of adults intersect... This is a grand myth of love spun with one's own feelings and the survival of the universe at stake.

Since childhood, Kazuhiro Kitase has been able to dream of a different world. He can return to reality by falling asleep or dying, and he can pick up where he left off by sleeping again. For years, he has had many adventures alongside Mariabelle, a beautiful elf who works for the Sorcery Guild. On one of their escapades, they come across the lair of a dragon taking care of its eggs. They inadvertently wake the slumbering beast, who promptly reduces them to ashes. For Kazuhiro, it is merely a temporary setback, as he can simply go back. However, he is shocked to find Mariabelle herself safe and sound asleep next to him. Kazuhiro realizes that his dream world is an alternate reality altogether. In the meantime, he makes the most of this bizarre circumstance, introducing Mariabelle to the sights and wonders of Japan. Now, with their time together spanning two worlds, their real adventures have just begun!