Arlequina, alias Harleen Quinzel, functions as a central antagonist in *Batman Ninja*. Transported to feudal Japan alongside the Joker and other Gotham City villains by Gorilla Grodd's time displacement machine, she serves as the Joker's fiercely loyal accomplice. She actively aids his conquest as the villains establish themselves as warring feudal lords.

Her tactics feature significant deception, including posing as a distressed peasant woman to lure Batman into a trap during an assault involving a transforming mechanized castle. This ruse nearly succeeds before Batman escapes. Following a confrontation on the Joker's ship, an explosion erases her memories and the Joker's, leading them to live briefly as peaceful farmers. This amnesia ends when specially planted flowers bloom, releasing toxins that restore their memories and villainous natures.

Regaining her memories, Arlequina rejoins the Joker to retake their fortress from Gorilla Grodd. She participates in the climactic battle where the Joker merges multiple castle robots into the colossal entity Lord Joker. During this final confrontation, she engages Catwoman in combat but is ultimately defeated. Following the villains' overall loss, she is returned to the present day and apprehended.

Her core personality remains intensely loyal to the Joker, unpredictable, and deriving enjoyment from chaos and violence. This iteration demonstrates heightened proficiency in disguise and combat tactics within the feudal Japanese setting.