Keita Aono is an ordinary high school student who loves to chat with his friends about military technology and the girls in their class. One day, Keita is surprised and delighted by a new transfer student in his class, his childhood friend Hinoki Sai. But when Keita tries to catch up with Hinoki after school, he accidentally wanders into Bottom World—an underground amusement park whose opening was canceled due to an unexplained tragedy. As Keita explores the area, he eventually finds Hinoki in the cockpit of a strange robot. She is here on behalf of Akamatsu Industries, a company contracted with the secretive international organization Mode Warp to investigate strange cases of violence worldwide. After joining Hinoki in the robot, the pair attempt to defend themselves against the various attractions of Bottom World, which have come to life and become violent. However, they are unable to escape until a man with transforming powers—dubbed Betterman—joins their struggle. Faced with an enemy he does not understand and a slew of mysterious new technology, Keita joins Akamatsu Industries in a fight against a force they call Algernon.

Energetic and thrill-seeking sixth grader Toppa Bashin has his mind set on only one thing—the card game Battle Spirits. Bearing a ruby pendant inherited from his missing father, Bashin heads to school every day with excitement: not for academics, but for card battling, much to the chagrin of his peers. One day, Bashin encounters J, the child prodigy champion of Battle Spirits, who bears a similar pendant. Star-struck, Bashin challenges J to a battle. However, the battle he gets is one he did not anticipate; the two are teleported to a mysterious arena in the sky—the Isekai World—where Spirits from the game become real. Feeling that his dream is finally within arm's reach, Bashin dives headfirst into the Isekai World, encountering other card battlers with extraordinary pendants. While making his way to the top, he slowly realizes that there is more to Battle Spirits than he ever imagined.

Like every card game enthusiast, Hajime Hinobori has always wanted to see the Spirits from his cards come to life and witness them in real combat. This dream is successfully realized by Hajime's scientist parents, who develop an augmented reality system that revolutionizes the competitive scene of Battle Spirits. Curious players from across the globe travel to partake in this innovative battle system. With his sight set on becoming the champion of this new form of Battle Spirits, Hajime encounters many colorful and quirky rivals, including eccentric diva Kimari Tatsumi and arrogant prodigy Tegamaru Tanashi. Along this journey of self-discovery and card-gaming shenanigans, there are no ordinary days in the lives of young heroes striving to take the crown!