One day, when Remu Mikage is on a video call with his sister, Shiki, who has traveled to the futuristic Okinotori-island Mega Float City for school, she confesses that both the audio and visuals of her are completely artificial. In order to be more efficient in her studies, Shiki has used neural-linked nanomachines to upload her consciousness onto a computer and is storing her physical body in a "body pool." While shocked, Remu is supportive of his sister's decision, until the disaster known as the "Early Rapture" happens. The Early Rapture causes everyone who has uploaded their consciousnesses to either fall into a coma or perish. Remu visits his sister's empty apartment one last time, but is shocked when Shiki arrives at the door. With no memory of her family or past, and being pursued by a violent group of researchers, Shiki and her brother are forced to flee using her newfound power of nanomachine manipulation.

After returning from the feuding realms of Gundalia and Neathia, Danma Kuusou and his companions continue their lives on Earth. Now, a year later, the virtual reality world of Bakugan Interspace has finally recovered from the alien invasion and has once again become a place for brawlers to gather and challenge themselves. It turns out, however, that whenever Danma's Bakugan, Pyrus Dragonoid, unleashes his might in battle, the Interspace experiences new disruptions. Unable to harness the incredible powers granted to him by Code Eve—the Bakugan Mother spirit—he struggles to maintain control over the Mechtogan contained within him. When it goes out of control, the mysterious mechanical entity wreaks havoc on the battlefield, attacking friends and foes alike. To make matters worse, Bakugan Interspace is at risk of being infiltrated again. An unknown mastermind is sending mutated Chaos Bakugan into the system in order to brainwash brawlers and take control of the virtual realm. In anticipation of the inevitable confrontation, Danma must find a way to keep the Mechtogan's destructive force at bay and rally the Battle Brawlers once again. [Written by MAL Rewrite]

Nagisa is a schoolgirl with schoolgirl tendencies, waking up late, rushing off to school and meeting up with friends upon the way. One morning Nagisa comes across a woman dressed in a strange uniform who seems to stare at her, unnerving Nagisa. Later that day, whilst staring out the window, Nagisa becomes aware of a ball bouncing by itself which flings itself towards her window seat, shattering the glass yet not harming her... Turning back to the front she finds a gaping mouth bristling with teeth inches from her face and no-one else about. She screams and the world returns to normal with her standing and the centre of curiosity of her class... why did she scream?

Virtual Reality and the arrival of Circlet Technology has changed people's lives. A new competitive electronic sport called Circlet Bout emerges, and schools duel to determine the strongest Circlet Bout Club and player. One day, Yuuka Sasaki gets mistaken for a challenger and battles against Chikage Fujimura, the best player in Japan, tying the intense fight despite her inexperience. These events lead to her passion for the sport, deciding to become a Circlet Bout player. Two years later, Yuuka moves to Tokyo and enrolls in Union School, a place where she can practice and pursue her dream of fighting Chikage again. After her arrival at the Union School, she discovers the club closed. Now her first goal is to help the athletic Miyuki Kasahara and club manager Ayumu Aizawa reopen Union's Circle Bout Club and return it to its former glory.