Bruce Wayne operates as the vigilante Batman in Gotham City, leading the Bat-Family. Previously, Gorilla Grodd's Quake Engine transported him and allies to Feudal Japan, where they confronted warring factions and the Joker's schemes before returning to the present.

After this return, Batman discovers Japan has vanished from reality. A portal manifests over Gotham, raining Yakuza soldiers. He investigates this temporal disruption, uncovering Ra's al Ghul's manipulation of reality using an advanced Quake Engine. Ra's created an alternate Japan, Hinomoto, ruled by the Hagane Family, which includes corrupted versions of Justice League members. Batman coordinates the Bat-Family—Nightwing, Red Hood, Red Robin, and Robin—to counter this incursion, deploying tactical plans and specialized technology. He formulates "Science Ninja Art" techniques tailored to exploit each Yakuza League member's weaknesses, reflecting his contingency-based strategizing.

His personality remains stern and mission-focused, prioritizing the protection of Gotham and allies. He demonstrates care for his allies, particularly Damian Wayne, whose altered appearance serves as an early indicator of the timeline corruption. He collaborates with unexpected figures like Wonder Woman (Daiana Amazone), who resists the Hagane, and reluctantly accepts aid from the Joker during a critical aerial confrontation. His equipment includes upgraded vehicles like the Bat-Phoenix and mechanized suits, alongside traditional tools such as grapple guns and blades.

A significant confrontation occurs with Kuraku, the Yakuza Superman. Batman employs a combination of technology and psychological insight to subdue him, emphasizing Kuraku's deviation from Superman's ideals of hope and highlighting his respect for the true Superman's legacy. Batman ultimately defeats Ra's al Ghul by disrupting the origami-based reality-warping system, restoring the timeline and imprisoning Ra's. The narrative focuses on his role as a tactical leader amid surreal threats.