Winning the high school team tournament was a great accomplishment for the Mizusawa members. Each of them has made great strides in improving themselves, and the victory symbolizes how far they have come. But after accomplishing one goal, their individual aims are within reach. Chihaya Ayase has her sights set on Shinobu Wakamiya and the title of Queen, and now that Taichi Mashima has made it into Class A, he can finally compete against Arata Wataya. Everyone in Mizusawa wants to get better, and there is no telling what the future holds if they keep trying.

All his life, Shiki has been surrounded by machines. At Granbell Kingdom, a long-abandoned amusement park, he is the only one of his kind around. That is, until Rebecca Bluegarden and her feline companion Happy arrive, unaware that they are Granbell's first visitors in one hundred years. Their goal is to make fun videos for their B-Cube channel, but what they find instead is a friend in the socially awkward Shiki. When Granbell becomes too dangerous for the three of them, they set off on an adventure through the Sakura Cosmos. They hope to make more interesting videos and even find the elusive goddess Mother, while Shiki wants to make more friends, spurred on by the words of his late grandfather. Of course, the journey will not be easy, as no one has seen Mother before, but Shiki is determined to reach his goal and explore the boundless reaches of space together with his new friends.

Now in possession of the Edens Zero, Shiki Granbell has gathered the Four Shining Stars. With the help of his new friends, Shiki will be able to breach Dragonfall—the border of the Sakura Cosmos swarming with mechanical dragons. Once that is achieved, he can continue his quest to find the goddess Mother. Before the Edens Zero crew can advance their journey, they notice a mysterious warship following them. Upon learning that the ship—the Belial Gore—belongs to Drakken Joe, Shiki and his crew attempt to infiltrate it, intent on figuring out why the Dark Alchemist is after them. In the process, the Edens Zero is taken hostage by Drakken's subordinates. Though they are in a tight situation, Shiki refuses to back down. Working together with his friends, Shiki will have to take down the Dark Alchemist if he hopes to make it out of the Belial Gore alive.

Shun Asanaga is a 15-year-old junior high school student with an optimistic and bright personality. One day, he finds a mysterious crystal in the office of his father, who is a scientist and businessman. When Shun touches it, the world becomes distorted, and he is sent into the world of Endra. Emilio, a prince of the kingdom of Endra, is nearing his 16th birthday and despises the reigning king, Delzain. Since Emilio is now at the age when he can inherit the throne, he takes up a weapon and attempts revenge. However, because Emilio is too weak, he is captured by Delzain and put in prison. When Emilio is in grief, the wall of his cell becomes distorted and Shun appears from there with two goals: return to his own world, and complete Emilio's revenge. What future lies ahead for the two boys trying to survive in Endra, yet raised in two different worlds? (Source: MAL News)