The show, Gotham (on Fox) is a take on the story of Batman, beginning with the death of Thomas and Martha Wayne. Season one focuses on the reign of Falcone, and looks at the origin of many pivotal players in the Batman stories, Bruce Wayne and Jim Gordon among them.

When Jim entered the GHPD, he was the son of a well-respected former Gotham prosecutor. When asked why he didn’t follow his father’s path to the law, Jim says something along the lines of how his desire is to enforce the law physically, rather than through the courts.

Jim is one of the few (maybe only) ‘by the books’ cops. ‘By the books’ refers to someone that enforces the letter of the law to all people of Gotham. Whereas to other cops, all means ‘street people’, to Jim: all means all.

The difference in his definition of the word ‘all’ gets Jim in a lot of trouble. People such as the mayor, Falcone, and other major players in the upper echelon of the Gotham crime scene were used to getting away with many things. They were able to use the law, the police, and other parts of the city to their own advantage. Until Jim.
   There’s a scene where Jim arrests both Falcone and the Mayor, and in doing so turns the police force against him. A few episodes later, the same Mayor (or maybe police chief - no charges or consequences were actually enforced against anyone) and Jim have a multi-layered altercation.

In the altercation, a man is killed by hired assassins. The murder weapon was the gun of Jim Gordon. Jim had entered the guy’s apartment in search of the truth in Wayne murder, after vowing to Bruce Wayne that he’d catch the true killer. The assassin knocked Jim out, took his gun, and killed the guy that owned the apartment.

The problem was that Jim shouldn’t have ever entered the apartment. The Wayne murder was a closed case. A suspect had already been found guilty. Problem solved...or so it seemed. The issue was that the solving of the crime was done at the surface level, to satisfy the public. The truth that someone had intentionally committed the murder, that that person was still on the loose, and that the higher ups in the city were covering that up didn’t sit well with Jim. This meant, going behind his boss, his partner, and the status quo to get to the bottom of the case.
   When Jim entered the apartment - without permission or authority - shit hit the fan. Jim talks to the apartment owner, discovers that his intuition is correct and there’s much more to the case than first appeared. He’s on to something, and then assassins show up. One overtakes him, knocks him out, takes his gun, kills the guy, and flees the scene. A few hours later, Gordon wakes up in the apartment alone. He discovers the owner of the apartment dead and sees his gun on the floor. Jim knows this is a problem, but - like the man of the law he is - calls it in anyway. In the aftermath, he finds himself face to face with the mayor, this time on the receiving end of the bureaucratic backlash.
   The mayor uses the upper hand to make a public statement. In his statement, he claims the apartment owner overtook Gordon, grabbed his gun, and committed suicide. This further isolates Jim.

Jim finds himself doubly fucked. Not only is it affirmed that his intuition about the Wayne murders is beyond correct, the cover up goes as high as the mayor.
   Another problem: Jim’s desire to do good and make change rises; he realizes it’s even more important than he originally thought, but he has even less ability to do something about it than he did before.
   By taking the risks to do something, by speaking out against the system, by attempting to right wrongs and help those that truly need it - thereby giving a voice to the voiceless - Jim is punished. He’s sent to Arkum Prison to watch over the insane. His talents thrown into the prison. He’s encouraged to resign. Attempted to be pushed out. They take Jim and try to make a public mockery out of him.
   But he refuses to play dead. He refuses to give up. He refuses to move or take the easy road.
   He decides to fight.
   I am Jim Gordon.