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.