Gordon then confronts Frank, who admits ordering the hit because Peter threatened to expose the Court. However, he hesitates and decides to leave only to be ambushed by Ra's and assassins from the League of Shadows posing as guards. He subsequently realizes that Mario beat the virus through a cure in the files, had himself tested and told Zsasz to free him so he could arrive at the wedding and look like a jealous ex. Mario leaves but Gordon notices a band-aid in his neck. After deciding, he chooses to save the boy and the couple fall from the bridge, killing themselves. Will the Joker, Riddler, Catwoman and some of the other Bat-villains really appear at some point?
They take him to the underground of the penitentiary while Gordon and Alfred investigate upstairs. Jim's real reason for becoming a bounty hunter was because he had become tired of losing the things he cared about in his effort to save Gotham when it was apparent it did not want to be saved. Meanwhile, Azrael came to his feet, and although Gordon got out his gun to shoot him, his gun had no bullets left. Flamingo immediately appears armed with a chain and initiates a series of attacks against him. With the knife at her neck, the Ogre orders him to lower his weapon, and Barbara tells Jim to leave them alone, but Bullock distracts Skolimski from behind and Gordon shoots him in the forehead, killing Skolimski, avenging the women he has killed and ending his killing spree. Despite not having the support of Alfred, Bruce accepts hosting Selina.
Gordon goes to visit Pyg but finds him gone, a guard dead and "It's been fun James - Lazlo" written in the wall with the guard's blood. In the GCPD, Gordon, Bullock and Alfred begin interrogating Bruce in an attempt to destroy the Shaman's brainwash. Gordon and Alfred manage to defeat the guards and reach the room. Jim is later reinstated as a Detective. At a diner, Bruce informs Gordon of what they had learned, and Gordon shares his suspicions that he suspected that the Philosopher was in charge of Pinewood, so he quickly begins to plan a way to prevent Karen from being sent to Blackgate since she was the only person who could identify him. Gordon and Bullock arrive to find an already dead Cicero and Jerome manages to escape.
The two then leave, with Butch telling Gordon, Bruce, and Alfred good night.Gordon tells Bullock inside his office that they needed to bring in Strange. To the astonishment of the group, Fox showed them a photograph of the old Gotham cricket team where Thomas stood by his friend Hugo Strange, otherwise known as " The Philosopher".Gordon, Bullock and several officers of the GCPD come to Arkham Asylum with a court order to inspect the office of Hugo Strange. Gordon arrives with Falcone, demanding to know where he is. At Jason's apartment, Gordon and Bullock arrive, finding it empty. Later at Blackgate during the screening of a film, Gordon cautiously sits down to the watch the film. Jonathan tries to compel him to kill himself but Gordon resists. Gordon and Bullock interrogate the mole but fail to convince him until Lee doses him with a truth serum and Dove reveals that Dwight and the cultists are planning on broadcasting a message at a TV station. Jim quickly goes to her penthouse, and asks Selina if the sketch looked like the man Barbara had left the ball with.After learning that the Ogre frequented a brothel called The Foxglove, an extremely exclusive place that was only never used the same place twice. Given that Lovecraft could not be found anywhere, Dent gives Jim the addresses of several of Lovecraft's condos that he had under the name of his mistress to try to find him.
The hallucinations end as Mario manages to wake him up. She dies on Cobblepot's arms. At Artemis, Jim is denied access, but Barbara appears and offers help to knowing how much he cared about the Wayne case. However, Gordon receives a threat from Professor Pyg on the phone if he enters and puts the wounded officer's voice. One night when an escapee was robbing a pharmacy Jim attempted to subdue him but was forced to push him in front of an oncoming truck, thus killing him.
During the events of the No Man's Land crisis, Jim has a brief fling with his ex-fiance Barbara, which led to her getting pregnant. He then takes out a gun and tells Gordon which one of them loves the most so he can kill her to get revenge for Alice's death. Afterward, Jim is called by Bruce who hastily explains the situation, and Gordon leaves to meet him. Gordon instantly deduces that the killer is Mario. Suddenly the man tries to kill him with piano wire, and the two intertwine in a violent battle until finally, Jim emerges victorious. After asking him if his interrogation had gotten him any leads, Barnes showed him the video of the robbery that had taken place at an auction house, with Gordon recognizing Selina Kyle in the footage. The GCPD is investigating the couple's death and upon seeing that Gordon saved the boy, Nathaniel Barnes tells Harvey Bullock to put an all-points bulletin on Jim Gordon. Due to the illegal search, Essen removes Gordon and Bullock from the murder investigation. After questioning him, he tells them to go see a Chinese bookkeeper by the name of Xi Lu. Gordon interrogated Jacob Skolimski and found out that the Ogre was actually his son, and that his son wouldn't be capable of murder. Gordon and Bullock surround Fish and try to get back Strange but Victor Fries arrives and creates an ice barrier that lets them escape while an infected Gordon slams the barrier. When he leaves, he comes back with Commissioner Loeb who orders him to leave.