Post-Crisis
After serving in the United States Marine Corps, James Gordon starts his law enforcement career in Gotham. As a young cop, he shoots and kills a corrupt cop and his wife in self-defense in front of their son. Gordon's transfer to Chicago is arranged by Captain Gillian Loeb, in an attempt to keep himself and his fellow corrupt cops from being exposed. Loeb threatens the child's life in order to force Gordon to comply with the transfer.
During Gordon's tenure in Chicago, he struggles with his wife over conceiving a child while taking night classes in criminology. He becomes a minor celebrity after a foiling a late-night robbery attempt. When he decides to investigate a corrupt fellow officer, however, the officer and his cronies assault him, and the police department discredits him in order to cover up the scandal. Gordon uncovers evidence of rigging in the city council election and brings down two of his fellow officers, which leads to his commander transferring him to Gotham.
Gordon is transferred back to Gotham City after spending more than 15 years in Chicago, discovering his wife is pregnant with his son shortly after. A man of integrity, Gordon finds that Batman is his only ally against the corrupt administration, which is in league with mob boss Carmine Falcone. Gordon's relationship with Batman is kept out of the public eye whenever possible. He retaliates against an intimidation attempt by corrupt fellow officers with equal violence. He has an extramarital affair with a fellow detective, Sarah Essen. Gordon breaks off their affair out of guilt. Falcone sends his nephew Johnny Viti to kidnap Gordon's wife and son; Batman saves them, however, and helps Gordon expose police commissioner Gillian B. Loeb's corruption. After Loeb resigns, Gordon is promoted to captain.
While still a lieutenant, Gordon convinces Loeb's successor to implement the Bat-Signal as a means to contact Batman and also to frighten criminals. The first Robin, Dick Grayson, becomes Batman's sidekick. Gordon initially disapproves of Batman recruiting a child to fight dangerous criminals, but grows to not only accept the boy but trust him as much as he does Batman.
Gordon quickly rises to the rank of commissioner after he and Batman weed out corruption within the department. After the death of his brother and sister-in-law, he adopts his niece, Barbara. Soon after he adopts Barbara, he divorces his wife, who returned to Chicago with their son James Gordon Jr., while he retains custody of Barbara, who eventually becomes Batgirl. Gordon quickly deduces the heroine's true identity, and attempts to confront her about it, going so far as to search her bedroom for proof. However, he is partially dissuaded from this belief, when Batman has Robin dress up as Batgirl while Barbara is on the roof with her father. Gordon continues to believe his daughter is indeed Batgirl, but does not confront her about it.
The Joker kidnaps Gordon after shooting and paralyzing Barbara. He then cages Gordon in an abandoned amusement park and forces him to look at photos of a wounded Barbara in an effort to drive him insane, thus proving to Batman that even seemingly normal people can lose their minds after having "one bad day". Batman eventually apprehends the Joker and rescues Gordon. Despite the intense trauma he has endured, Gordon's sanity and ethical code are intact; he insists that Batman apprehend the Joker without harming him in order to "show him that our way works".
Soon after Sarah Essen returns to Gordon's life, they rekindle their romance and get engaged. However, Essen cannot comprehend why Gordon needs Batman so much, which occasionally puts a strain on their relationship. Later, Gordon suffers a heart attack; his chain-smoking over the years has weakened his heart.
Shortly before their planned wedding, Arnold Flass (Gordon's former partner) beats Gordon and kidnaps James Jr. for ransom in exchange for letting a corrupt judge go free. Batman saves James Jr., while Gordon, Essen, Flass, and the judge are trapped and must work together to escape.
After Bane breaks Batman's back, Jean-Paul Valley and Dick Grayson assume the role for a brief period and do not tell Gordon about the switch. Gordon is removed from his post as commissioner and replaced by his own wife, due partly to his own disinclination to trust Batman.
During the Cataclysm storyline, Gotham is devastated by an earthquake and isolated from outside assistance. Inside Gotham, Gordon struggles to maintain order in the midst of a crime wave. Batman is mysteriously absent for the initial three months, and Gordon feels betrayed. He forges an uneasy alliance with Two-Face, but the partnership does not last; Two-Face kidnaps Gordon, putting him on trial for breaking their "legally binding" alliance. Gordon escapes, however, and later meets with Batman once again. In this confrontation, Gordon berates Batman for letting Gotham "fall into ruin". Batman offers to prove his trust by revealing his secret identity, but Gordon refuses to look when Batman removes his mask. Eventually, the two repair their friendship.
After the earthquake, the Joker kills Sarah Essen. An enraged Gordon barely restrains himself from killing Joker, shooting the madman in the knee instead. Not long afterward, Gordon is shot by a criminal seeking revenge for a previous arrest. Though seriously injured, he survives, and eventually makes a full recovery.
Gordon retires from the police force after having served for more than 20 years. Despite being retired, Gordon often finds himself drawn to a series of life-and-death circumstances, such as the Joker sending him flowers during Last Laugh, or being contacted by the temporarily reformed Harvey Dent to stop Batman from killing the Joker, to being kidnapped by Francis Sullivan during the Made of Wood storyline. After the attack by Sullivan, Batman gives Gordon an encrypted cellphone, the so-called Batphone, in case he needs to contact him, which also carries a transmitter in case of trouble. Commissioner Michael Akins has taken his position, with many officers expressing reluctance to follow him out of loyalty to Gordon.
After Barbara requires surgery to counter the life-threatening effects of the Brainiac virus, Gordon visits her in Metropolis. She reveals to him her current role as Oracle, as well as her past as Batgirl. Gordon admits that he knew of her identity as Batgirl, but is pleasantly surprised to know of her second identity as Oracle.
While mourning the death of Batman, Gordon and his daughter are attacked by several of Batman's enemies, who have been resurrected as members of the Black Lantern Corps. They are rescued by the current Batman, Robin, Red Robin, and Deadman, but are later attacked by Batman and Red Robin's parents, the reanimated Flying Graysons, and Tim Drake's parents.
Gordon is tricked into shooting at an unarmed suspect in an underground train station, resulting in a train derailing and Gordon being arrested. While incarcerated in Blackgate Penitentiary, Gordon is visited by his son, who makes arrangements to leave his father's cell open and provide him with an opportunity to escape Blackgate. Gordon decides to remain in prison, concluding that Gotham is still worth saving and simply musing that he may just be getting old and made a mistake. Gordon is released as the final assault on Gotham begins, proceeding to rally all of Gotham to stand up and take back their city to aid Batman for everything he has ever done for them.
Following Bruce Wayne's apparent death in a battle with the Joker, Gordon takes up the mantle of Batman using a mecha-style suit to fight crime in Gotham City. Gordon later meets the de-powered Superman when Clark comes to Gotham to investigate evidence that the weapons being used against him were created in Gotham, but their initial meeting results in a fight as Superman does not believe that Gordon is the new Batman and Gordon doubts Superman due to his working with Luthor. Although Gordon doubts Superman's abilities due to his powerless state, he eventually works with Superman to stop Vandal Savage stealing an artificial sun created in Gotham to use as part of his latest plan, their alliance helping Gordon recognize Superman's continued merits as a hero while Superman in turn acknowledges that the new Batman gets the job done. Gordon later works with the Justice League to investigate the death of a large monster, the heroes noting after the case has concluded that Batman's high opinion of Gordon's abilities as a detective were well-founded. Despite Gordon's best efforts, political issues in the department result in Mr. Bloom destroying his armor and mounting a massive assault on Gotham after seriously injuring Gordon, prompting the amnesic Bruce Wayne to try and reclaim his role as Batman. The crisis concludes with Bloom defeated by the returned Batman using some of Gordon's equipment while working with his old ally. The return of the true Batman prompts the GCPD to shut down the program and restore Gordon to his role as commissioner.
Gordon seeks help from his estranged son James Jr. to work alongside him and Batman to take down the doppleganger known as The Grim Knight. Gordon is kidnapped by The Grim Knight since The Batman Who Laughs seeks to recruit him as an ally, only to rebuke his offer. He is later able to escape. Learning that Batman has been infected by the Batman Who Laughs, Gordon and James are tasked to protect the Batcave from the Grim Knight, who is on his way. With each one donning a Batsuit, they briefly get the jump on the Grim Knight. However, the Grim Knight uses Gordon's own words against him and seemingly sway James Jr. to his side. As he is strangled by the dark Batman, Gordon notices a vial of toxin poured into the water and the Grim Knight begins to drown him in the water; taking several gulps of the poisoned water, Gordon is saved by James stabbing the Grim Knight repeatedly in the shoulder and back. Gordon consoles his son and affirms that he loves him. However, due to being subjected to a small dosage of the toxin, Gordon becomes corrupted. Batman is able to get help from Superman in capturing Gordon and the other infected heroes until a cure can be found.
James Jr. develops a split-personality disorder, murdering redheads and dressing them up as Batgirl out of jealousy. Finding out what he did, he commits suicide by jumping off of a lighthouse. Blaming Batgirl for James' death, Gordon lashes out of her.
Gordon retires from public service as a result of his son's death and agrees to look for Joker on behalf of a secretive organization, with his daughter Barbara providing intelligence and communications support. He knew his daughter was Batgirl and only blamed her out of grief for his son.
