J. J.'s 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 was said to be currently living with his mother in Chicago until Scott Snyder's Skeleton Cases story.
As a child, J. J. showed tendencies of a sociopath; he was suspected to have killed others who taunted him. He left Gotham and subsequently disappeared. It is heavily implied that he went on a killing spree across the country.
As J. J. continued going about killing people, he realized the law would eventually catch up with him. He subsequently put himself in a programme to test a new drug which could treat his condition and help feel empathy. This did indeed help him for a while, but J. J. began to reason that empathy was a weakness, and secretly altered the drug to blunt his empathy further. Upon seeing Batman on a televised news report and realising it was Dick Grayson, he decided to return to Gotham and face him.
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, J. J. This troubling assumption begins to trouble Gordon and soon he becomes haunted by the visions of past unsolved case files that involved murdered children.
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 apprehended the Peter Pan Killer when he attempted to abduct a young J. J.
Now after 15 years, Gordon heads to Blackgate to interrogate the Peter Pan Killer before he was released from prison. Gordon wanted to find out why the killer didn’t go through with kidnapping J. J. The killer reveals that he was going to kill Gordon Jr. rather than abducting him because J. J. gave the killer an ominous stare when he entered the boy’s room. The killer also reveals that he murdered a young girl who was friends with Oracle before he visited Gordon’s apartment.
This revelation causes Gordon wonder about his son’s innocence and what exactly happened to the young girl. Oracle has always been under the assumption that J. J. murdered her friend because she saw him playing with her friend’s house keys. Gordon has heard this story from Babs before but now he doubts if Babs’ story is actually true. There is a possibility that the killer took the young girl’s keys and dropped them at the Gordon’s apartment by accident. After his conversation with the Peter Pan Killer, Gordon threatens the killer that he will be followed at all times in order to prevent another murder.
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 for a psychological evaluation and the doctors clinically diagnosed him as mentally unstable in regards to exhibiting psychpathic behavior. However, the doctors prescribed an experimental medicine to help James in stabilizing his emotional imbalance.
James also overheard Oracle's convictions 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. For a while, Gordon feels this extreme sense of relief that his son is misunderstood but he is changing for the better. When Gordon reaches his apartment, he finds a trail of blood. Gordon follows the trail to James Jr.'s old room. The trail ends in James' closet. Gordon opens the door and finds the body of a schoolyard bully that James Jr. fell victim to when he was young.
It seems everyone was right about James Jr. even though Gordon tried to give him the benefit of the doubt. Gordon immediately goes to the clinic and finds Dr. Thompkins. Gordon confronts Leslie by demanding to know where his son is. Leslie informs Gordon that his son is a model volunteer because anything she asks him to do, he "happily" does. Over time, Leslie has given James Jr. more responsibilities like making "nutrition runs" for newborn babies who come from poor families. Gordon doesn't want to panic Leslie by telling her what he had found at his apartment so he humbly asks her to call him the moment James comes in for his shift. Leslie agrees to Gordon's request and she tries to calm his worries by showing him James' office.
Leslie flips on the lights in James' office and gives Gordon a tour. As Leslie professes how great James is, Gordon on the other hand, can't believe that Leslie would be so naive to willingly put her full trust in someone like James. Gordon peers around the office and finds a vile of James' medicine. The medicine is called Diaxemene which is designed to release a chemical in the brain so the patient can feel empathy. Gordon takes a pill from the vile, thanks Leslie for the tour and makes his way to Barbara's place at Kord Tower.
Gordon gives Barbara the 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.
Gordon leaves Barbara to her work while he heads back to the clinic. 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 Gordon's cell phone. 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 putting his pills in the baby formula and giving it to all the newborns thereby ensuring their development into becoming psychopaths.
Just as Gordon reached the clinic, he is stopped by Det. Bullock who has some really bad news. Bullock says the Joker has escaped Arkham and something horrible has happened to Gordon's ex-wife. Gordon acts quickly by warning Leslie about James then he calls in a small task force to station themselves at the clinic and wait for James to return. Gordon must put the hunt for his deranged son in the hands of his brothers in blue while he accompanies Bullock. Bullock tells Gordon that he received an anonymous phone call from someone who said Barbara Gordon is going to die at the Gotham Plaza Hotel. Gordon and Bullock reach the hotel room where Barbara was staying at and as Gordon entered, he notices a light coming from the bathroom. Gordon falls to his knees in tears 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 while Bullock calls in Oracle and tells her what has just happened. 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. Oracle keeps James busy enough for Dick and her father to come to her aid, and a heartbroken Jim disowns his son and has him committed to Arkham Asylum.
James Gordon Jr. made a cameo - in Arkham Asylum - in the new Batman title by Scott Snyder, who stated he plans to continue James' storyline that he started in his previous run on Detective Comics, saying "As for his presence in Gotham, he's someone I have some fun (dark and twisted) long-term plans for."
- He was born October 12.
- A similar man appeared in the Batman: Black And White story An Innocent Guy (which was later included in the 2008 reprint of Batman: The Killing Joke, where he claimed to be innocent, but desired to kill Batman just to prove whether he was a good man as well as plotting how to do so.