In Batman Ninja vs. Yakuza League, Gordon serves as the Commissioner of Police in Gotham City. His role is primarily concentrated in the opening act of the film, where he is depicted as a figure grappling with an unprecedented and bizarre crisis. Following the events of the previous film, his daily reality has been disrupted by a strange phenomenon: members of the Yakuza literally falling from a portal in the sky. Gordon is the one who explains to Batman that these incursions have become a regular occurrence, happening every day.

The Commissioner’s personality in this sequel takes on a more comedic and exaggerated tone compared to some of his more stoic portrayals. He is shown actively leading the police force in fending off the initial waves of Yakuza attackers, often with assistance from the Bat-Family. However, beyond his duty-driven actions, he displays a notable sense of panic and anxiety. This manifests in moments of exasperation, such as when he humorously berates the heroes from a rooftop, demanding they come down and assist with cleaning up the city. As the scale of the threat becomes clearer, particularly when witnessing the full scope of Ra's al Ghul's power raining down from the sky, Gordon's demeanor shifts to one of genuine terror, emphasizing his role as an ordinary man overwhelmed by extraordinary events.