Bakugan Interspace is a virtual reality system, where players can brawl against each other and take part in tournaments. Initially designed to help practice and enhance Bakugan skills, it quickly became a meeting place for many enthusiasts. During one of Danma Kuusou's duels, the Interspace crashes, and he gets knocked out cold. Before regaining consciousness, he experiences a vision of Bakugan at war with each other once again. The explosion of energy that accompanied Danma's fight and caused the shutdown of the system sends shock waves across the galaxy, attracting the attention of the Twelve Orders, a Gundalian organization. They infiltrate Bakugan Interspace, looking for strong brawlers to join them in their upcoming war with another alien race, the Neathians. Danma and his companions—Shun Kazami and Chouji Marukura—soon find themselves caught up in an extraterrestrial war. However, distant as it may seem, the conflict threatens the very sovereignty of Earth and the future of the Bakugan race as well. [Written by MAL Rewrite]

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]

After the final downfall of the rogue Bakugan Naga, peace was brought back to Vestroia. With the help of Danma Kuusou, his companion Pyrus Dragonoid, and other Battle Brawlers, the Infinity and Silent Cores were combined and the realm was recreated. However, New Vestroia will not be given any respite as humanoid alien invaders, the Vestals, arrive and conquer the Bakugan world in one fell swoop. Armed with a fearsome machine capable of restricting Bakugan into their ball forms, they aim to enslave the race as a form of entertainment. Now, the only force standing in their way is the Bakugan Battle Brawlers Resistance—a group of humans, Bakugan, and Vestals who oppose the idea of annihilating a sentient race. Led by Danma, they must venture into enemy-occupied New Vestroia and repel the invaders, to assure the survival of the entire world. [Written by MAL Rewrite]

For centuries, the Iga and Kouga ninja clans have engaged in a bitter war. But when a ceasefire is ordered by the powerful warlord Ieyasu Tokugawa, the two clans are forced to put down their arms. Years later, Gennosuke Kouga, heir of the Kouga clan, and Oboro Iga, heir of the Iga clan, have fallen in love. Through marriage, both heirs aim to bring peace to the clans. But their hopes are dashed when flames of rivalry between their clans are reignited, and they are dragged into another war. Ieyasu's two grandsons have both claimed to be the next heir to the shogunate. To resolve this dispute, both the Kouga and Iga are ordered to send their 10 best warriors to fight in a bloody battle royale, with each clan representing one of the potential shogunate heirs. Two scrolls with the names of the fighters are given and are to be marked in blood upon the given fighter's death. The prize for winning is the favor of the Tokugawa shogunate for a thousand years. Torn between their love for each other and duty to their clans, Gennosuke and Oboro must ultimately decide the fate of their clans. [Written by MAL Rewrite]