When we first meet future police commissioner James Gordon (Ben McKenzie) in the pilot episode of “Gotham,” Fox’s new “Batman” prequel that premiered Monday night, he is in a tight spot. A mentally ill prisoner has seized a cop’s gun in the middle of Gotham’s police department and is holding an officer hostage in exchange for his medication. A dozen of Gordon’s colleagues have their guns drawn, ready to shoot the man. But Gordon, sensing a potential riot if that happens, manages to lull the agitated prisoner with a bottle of aspirin and get in close enough to disarm him, at great personal risk to Gordon himself.

It was a striking scene when I saw it this summer, and it is more striking now, after the shooting death of teenager Michael Brown in Ferguson, Mo., and the protests that followed. Gordon’s reluctance to use deadly force in that scene, or later in a chase even when a fleeing suspect is firing a gun at him, is meant more to link Gordon to the superhero his future self will work with — Batman is famous for his antipathy to firearms — than to make a statement about contemporary, and increasingly militarized, policing. Gotham, after all, is a fictional city out of time with our own.

But contemporary politics gave the pilot for “Gotham” a new sting, and also cut to an issue at the heart of the show: How do you tell a story about a good cop’s utter loss of faith in the ability of any conventional institutions to keep a big city safe? How can James Gordon stay a good, principled police detective, someone who shares Sheriff Andy Taylor’s decency if not his Mayberry setting and policing challenges, while also becoming the kind of police commissioner who would choose to work with a vigilante like Batman?

“Cops deal in violence. When you start enjoying it, that’s when you’ve crossed a line,” “Gotham” showrunner Bruno Heller told me when we spoke about the show in Los Angeles in July. “[Future supervillain] Penguin (Robin Lord Taylor), for instance, is a psychopath, so feels no shame about the visceral enjoyment he gets from causing people pain. But he’s a phsyically weak person so he has to hide that love for violence behind a humble facade. [James Gordon’s partner] Harvey Bullock (Donal Logue), it’s instrumental, he has learned that you need to use violence, and he’s even learned that enjoying it occasionally doesn’t make him a bad person.”

Gordon tortures himself when a situation gets so far out of control that deadly force comes into it. When Bullock kills a suspect in the murders of Thomas and Martha Wayne (Grayson McCouch and Brette Taylor), Gordon feels guilty even though he did not pull the trigger. And when it turns out that the man was framed, Gordon’s instinct is to find the real killer, while Bullock wants to leave the case alone, both for the sake of his own reputation and for Gotham’s sense that the Wayne’s murderer is safely beyond reach.

Later, when Carmine Falcone orders Gordon to kill the Penguin, Gordon fakes the murder, hoping that his deception will satisfy Falcone and his kindness will neutralize Penguin. The episode suggests that it may not have been the right choice.

As well grappling with the necessity of violence to his job and the temptations of deadly force, Gordon will have to cope with challenges to his worldview. In the pilot for “Gotham,” Gordon finds himself face-to-face with crime boss Carmine Falcone (“The Wire” veteran John Doman), who suggests that the city is actually more stable when law enforcement and organized crime achieve a truce and a balance.

While he was walking me through the scene, “Gotham” director Danny Cannon told me that “I shot [Doman] from below because I wanted him to tower over Gordon. [Falcone] needed to tower over Gordon in that his ideology needed to tower over him.”

“One of the great, freeing things about talking about Gotham as opposed to a real city that you can tell truths about the way society works that would be libelous or impossible to tell in the real world,” Heller told me. “Any big American city has a degree of corruption and decadence and crime that can’t be articulated. It can’t be revealed. With Gotham you can make those connections between big business and politics and crime very clear, and naked, and sensational if you like. But they are true connections. No big city works without very specific and coherent lines of communication and control between politicians, crime, big business.”

Gotham is no Mayberry. But the questions the series and James Gordon’s career raise have deadly relevance to us, in cities big and, as Ferguson showed us, small as well.