In Arkham Asylum, Batman engages in combat with Gorilla Grodd while attempting to sabotage Grodd's creation, the Quake Engine. During their struggle, the machine malfunctions, causing both the asylum and Batman to disappear. When he regains consciousness, Batman finds himself on an unfamiliar path, realizing he has been transported to Feudal Japan.
His initial wonder turns into alarm as he is attacked by samurai intent on killing him. Further investigation reveals that his longtime nemesis, the Joker, has ordered this assault. Batman meets Catwoman and learns that the asylum inmates arrived in this era two years earlier, each having seized control of various territories in Japan, with the Joker becoming the supreme warlord.
To return to his own time and place, Batman must reactivate the Quake Engine, now housed within the ruins of Arkham Castle. However, he faces a significant obstacle as most of his equipment is missing except for his utility belt. This version of Batman, known as Ninja Batman, must navigate this unfamiliar world and confront his adversaries once more in order to make his way back to Gotham intact.