James is only seen as a toddler or small child during Batman's early year tales such as Batman: Year One and Batman: the Long Halloween. He is said to be currently living with his mother in Chicago.
Gordon gets a phone call from Harvey Bullock telling him to go to the Gotham City Aviary. When Gordon arrives, Bullock informs Jim that the aviary cages are all automated from the control room and there is some troubling video footage from the security cameras that Jim needs to see. Gordon sees the image of a man who resembles his son James Jr.
Later on that same day, Gordon invites Oracle for some coffee and talks to her about his findings. Oracle still sticks by her story and she leaves her father with lingering doubts but then James Jr. appears from other side of the cafe. James Jr. sits down with his father and explains his return to Gotham. James Jr. begins by apologizing to his father for the theatrics at the aviary. James tells the commissioner that his mother (Barbara Sr.) sent him to Arkham Asylum for a psychological evaluation and the doctors clinically diagnosed him as mentally unstable in regards to exhibiting apathetic behavior. However, the doctors prescribed an experimental medicine to help James in stabilizing his emotional imbalance.
James also knows how his sister feels about him and he swears to his father that he has never killed anybody. Gordon still doesn't know what to think about his son until James informs him about his volunteer work at Dr. Thompkins' clinic. James Jr. leaves the cafe and asks that his father will hopefully find it in his heart to forgive him.
This conversation causes Gordon to remember and wonder about his son’s innocence and what exactly happened to the young girl, Bess who was one of Babs' friends. Oracle has always been under the assumption that James Jr. murdered her friend because she saw James Jr. playing with her friend’s key to a science set they had bought together. Gordon has heard this story from Babs before but he doesn't want to believe that his son is a killer without enough proof.
Gordon later starts to think about a case that has haunted him for a long time. Fifteen years ago, Gordon was moving up the ranks within the precinct when he started investigating a string of eight murders that involved the Peter Pan Killer who would sneak into family homes and abduct children from their beds then murder them. Gordon never caught him.
Now after 15 years, Gordon trails a criminal who has just been released from Blackgate and who he suspects is the Peter Pan Killer. He confronts the killer and the killer reveals that he was going to abduct James Jr., at the Gordon's summer house, but when he confronted the boy, James Jr. simply turned around and told the killer that he knew exactly who he was. This leads Gordon to believe that the disappearance of Bess was the Peter Pan Killer's doing, because the event the killer described occurred on the same day Bess disappeared. This greatly eases Gordon's mind but he still has his doubts so he asks Dick to meet with James Jr. and see if he had really changed.
Dick meets with him and James seems calm and friendly. During his conversation, James says how he is going to see an old friend that they both knew, later that day. Dick is then called away due to a breakthrough in his case. It is then revealed that Jame's meeting with his friend is him dismembering and torturing him in his own basement.
Gordon, still suspicious of his son, goes to the clinic where James Jr. is volunteering at and asks, Leslie, James Jr.'s supervisor about him. Leslie tells Gordon that he is the model volunteer and that he even volunteered to start making nutrition runs for the clinic. James soon walks in and he thanks his father for stopping by.
Gordon asks to meet with Barbara and he gives Barbara a pill that he took from James' office and asks her to run a couple of tests. Barbara knew something was going on with James but she didn't want to rub in her father's face because she could see that Gordon still wanted to hold onto any hope of saving his son. Barbara figures the medicine is supposed to help James in treating or possibly curing his psychotic tendencies but Diaxemene is still in the testing phases and hasn't been approved by the FDA. Gordon is hoping he can convince James to undergo some blood work in order to make sure that he has been taking his pills.
Barbara breaks down the pill's components and she makes a startling discovery. James has reversed the effect of the pill and now the pill is designed to chemically induce apathy rather than empathy in a certain section of the brain. However, the dosage of James' pill is of such low grade that it wouldn't affect an adult. Barbara relays all of her findings to her father. Gordon can't understand why James would concoct a pill with such a low dosage then it hits him. Leslie made James responsible for the "nutrition runs" at her clinic. James has been or is going to start putting his pills in the baby formula and giving it to all the newborns thereby ensuring their development into becoming psychopaths.
Gordon reaches the clinic and bursts into his son's office to find he isn't there. Gordon does notice a box in the closet and when he opens it he finds the key that Bess had before she disappeared as well as countless other house keys, presumably taken as trophies. Bullock then finds Gordon and tells him the terrible news that the Joker has escaped from Arkham. Gordon immediately gets in his car and drives to the hotel the Barbara Sr. is staying at. While he is on his way he calls her and warns her about the Joker, during the call she hears a knock at the door and answers it. through the phone Gordon hears a crash and insane laughter as his ex-wife begs for mercy. Gordon reaches the hotel and bursts into his ex's room and goes into the bathroom. Gordon can only cry the word no, because he has found his beloved ex-wife nude in the bath tub with a crimson smile across her face.
Gordon rushes Barbara to the lab at Wayne Enterprises and he tells his daughter what has occurred. Oracle reacts by calling Dick and having him meet her father at the lab. Oracle runs a few tests on her mother while Dick injects the anti-Joker Venom. Fortunately, Gordon got to Barbara just in time to save her and the Joker Venom was a derivative of the original. Gordon at this point wants Joker's head on a pike for all the misery he has brought to the Gordons' but Dick convinces Gordon that there is no way the Joker could have escaped Arkham and found out where Barbara was so quickly. Dick promises Gordon that he will find Joker and make him talk.
Dick heads to Arkham and conducts a complete sweep of the crime scene. From what Dick could deduce, Joker didn't get very far from Arkham because Dick begins follow a trail of Joker's sweat which seems to be secreting Joker Venom. Dick follows the trail to an abandoned section of Arkham. At this point, Dick figures that Joker must have discovered Victor Zsasz's underground path which leads to the catacombs beneath Arkham. Zsasz used this path to escape Arkham so he could freely kill anyone he wanted in Gotham then he would make his way back to Arkham as if he had never escaped at all.
Dick finds Joker in a dank corner of the catacombs. He notices Joker mumbling to himself about being disappointed. Dick apprehends Joker and begins to interrogate him. Joker starts off by complaining about the fact that Dick isn't the real Batman by saying "You don't scare me little bird” and he isn't saying a word until the real Batman returns. Dick decides to beat down on the Joker until he reveals who he hired to attack Barbara Gordon. Joker laughs hysterically because according to him, the real Batman would have figured out that the Joker does his own dirty work and he would never send some errand boy to take credit for his fun. Dick finally realizes that the Joker was able to escape simply because someone needed him to be the scapegoat for the attack on Barbara Gordon and they were counting on Commissioner Gordon to retaliate by ending the Joker once and for all.
Back at the lab, Gordon sat by Barbara's side as Bullock escorted Oracle back to her apartment. Barbara eventually wakes up and when she laid her eyes on Gordon, she immediately began to scream for help. A doctor comes rushing and injects a sedative into Barbara. Gordon finally realizes that James injected the Joker Venom into his mother as a way to get back at her for institutionalizing him while at the same time he wanted Gordon to think the Joker was responsible for the attack on Barbara in order to bait him into killing the Joker. If Gordon knows how calculating his son can be then he would guess that James has already realized his plan to manipulate everything is falling apart which leaves only one person left for him to torture...Oracle.
Bullock drops Oracle off at her apartment doorstep and just as she entered her apartment, James closes the door right behind her. James and Oracle enter a discussion about on how depraved he is. James respects Oracle because she is the only one who can see him for what he is. Barbara replies to his compliment with a scoff. Oracle always knew James was disturbed and most of those people that he has already killed were actually victims rather people who had it coming. In short, Oracle realizes that James tries to find flaws or start something with another person just so he can justify as well as satisfy his violent tendencies. James smiles and his respect for Oracle's deduction has reached new lengths.
The New 52
James later reappears after the events of Flashpoint, and is shown encountering Barbara's friend Alysia. During an Arkham riot James escapes the asylum. He begins to mentally torture Batgirl. During Death of the Family, James has lead Batgirl to a skating rink where Joker holds their mother hostage. After deciding to kill the Joker, Batgirl meets up with Joker in a church, where Joker's plan is to marry her. However, James shows up threatening the Joker to release Batgirl or he will detonate to hand-held grenades. he also says that he has rescued his mother from the nail bomb in the skating rink. This allows Batgirl to take down Joker's henchmen. James then betrays Batgirl by trading her life for his mother's who was inf act never rescued.
After torturing Batgirl from afar, he meets up with his mother at the Gotham Bay Aquarium, the last place she saw her son smile. Batgirl interferes, just when James is about to shoot his mother. James tells his mother that Batgirl his in fact Barbara Gordon, her daughter. But she already new, she says, and shoots her son herself. Wounded, James escapes but is apprehended by Batgirl. James is giving Batgirl a concussion by hitting her in the head with a club. Dizzy, Batgirl defeats her brother. James then confesses why he does what he does. He tells them how she was always the favorite, "Perfect Barbara. Brilliant Barbara". And then it happens. Just as James is about to kill his mother with a knife, Batgirl throws a Batarang straight into James' left eye, making him fall down in the water. The body was never found, which suggest that he might've survived.
The Court of Owls
For more information see : A Court of Owls
While Batman investigates Dan Matthews, a guard at Arkham Asylum who maybe on the take, Dan in a desperate attempt to get away, opens several of the inmates cells. While the loose inmates attacks Batman, James is seen sitting calmly in his cell just before the Joker appears to come to Batman's aide and the pair work together to beat back the group of rampaging inmates.
The Dark Knight- Cycle of Violence
While under the influence of Fear Gas, Commissioner Gordon sees James Jr, in a straight jacket floating above the floor, along with a shot Barbara. The illusions of his children apologize for ruining James's perfect life. Though out the story James fights with the idea if sending his son to Arkham was a good idea.
Suicide Squad New 52
James Jr. survived his encounter with Batgirl and has begun appearing in the pages of Suicide Squad as an advisor of sorts to Amanda Waller. He has revealed through internal monologues that he is very attracted to her and may even love her.
The Dark Knight (2008)
James is one of Jim Gordon's children in The Dark Knight. He is depicted as being fond of the Batman. At the film's climax, he is chosen by Two-Face for death in revenge for the death of Rachel Dawes in which he blames Gordon. Batman saves him at the last moment, much like the ending to Batman: Year One. He is played by Nathan Gamble.