1975: Bruce Wayne is born
1981: Thomas and Martha Wayne are murdered. Alfred Pennyworth, Thomas Wayne's head of security, becomes appointed to be Bruce's legal guardian much to the dismay of Jacob Kane, Martha's brother, who blames Thomas for his sister's death and for his nephew being an orphan. James Gordon and Harvey Bullock try to catch the Wayne Killer, but get caught in a conspiracy by the mafia and GCPD where they frame a thief named Mario Pepper for the killings. Gordon confesses everything to Bruce after that and urges him to try not to loose faith in the city. Bruce then asks Alfred to train him.
1990: Dick Grayson, Barbara Gordon, Kate Kane, Tamara Fox, Timothy Fox, and Beth Kane are born.
1996: Bruce Wayne graduates from a university in Europe. Gordon is finally able to arrest Matthew Malone, the actual killer of Thomas and Martha Wayne. Bruce is angry when he learns from his childhood friend Ethan Bennett, who is now in the GCPD, that Catherine Klass, Bruce's childhood friend, and her boss Harvey Dent cut a deal with Malone to testify against Rupert Thorne in exchange for a pardon. Thorne hires a female assassin (disguised as a reporter) to kill Malone after paying Judge Faden to make the trial public, depriving Wayne of the chance to take his own revenge. Catherine is angry when she learns that Bruce intended to kill Malone at his trial, hinting that Thomas Wayne would be disgusted by Bruce. Bruce confronts Thorne at an underground establishment and tells Thorne that not everyone in the city is scared of him. Thorne dismisses the young billionaire as a harmless nuisance and has his thugs to beat him up in order to teach him a lesson. He tells Wayne that every important government official in Gotham is on his payroll, and that true power comes from being feared. He also mocks Wayne's late father, saying that Malone told him that Thomas Wayne "begged like a dog" as Malone killed him. After having his bouncers beat Bruce up, Thorne has him thrown out. In order to prove Thorne wrong, Bruce pays a homeless man for his coat and goes travelling, where he goes to Nanda Parbat to train with Ra's al Ghul and the League of Assassins.
1996-1999: Bruce trains with the League with Malcolm Merlyn. While there, Bruce and Ra's al Ghul's daughter Talia al Ghul become smitten with one another. After Ra's allows Malcolm Merlyn to return to the United States, Bruce wants the same thing as well. Ra's refuses to grant Bruce's request since he wishes for Bruce to be his heir and tries to get Bruce to kill a criminal who murdered a farmer for his land. Bruce refuses as he believes it is bad to kill and is angry at Ra's for trying to force this on him. Talia also gets angry at her father when she realizes that Ra's will never allow a woman to control the League and for forcing this on Bruce. Getting angry at Bruce and Talia, Ra's attacks Bruce with a sword. Bruce is forced to use a sword to defend himself from Ra's and is able to beat Ra's without killing him. Because of this, Bruce is allowed to leave the League and Talia decides to as well. Bruce tries to get Talia to return to the United States with him, but Talia refuses since she wishes to form her own path. Bruce is saddened by this and shares one last kiss with Talia before the two part ways. Around that time while Bruce is in the League, Alfred becomes a father to a girl named Julia Pennyworth and Lucius fathers a son named Luke with a woman named Tanya. Alfred asks Lucius to be Julia's godfather, which Lucius happily accepts.
- Ethan is trying to catch the Red Hood gang led by Red Hood One. Bruce meets with his maternal uncle, Philip Kane, but refuses to take over Wayne Enterprises. Edward Nygma, Philip's strategist, tries to get Philip to arrange Bruce's murder, in order to gain public sympathy and avoid a power struggle. After Philip refuses, Edward hires the Red Hood Gang to murder Bruce. In disguise once again, Bruce rescues Oswald Cobblepot from Red Hood One and takes a sample of the gang leader's blood, but fails to find who it belongs to. After Bruce has an argument with Alfred, the latter leaves and Bruce meets with Philip, who against Bruce's will, debuts him to the public. After Bruce retreats from the media, he meets with Nygma. He then goes to his brownstone, where he is attacked by the Red Hood Gang. The gang beats Bruce to a pulp, and the leader tells him that the Waynes' deaths changed him too. Bruce then retreats to Wayne Manor, where Alfred treats his injuries. Bruce finds the Batcave he fell into as a child and decides to use that as his lair.
- Red Hood One is revealed to be Jack Napier, a gangster for Rupert Thorne. Thorne gets angry at Napier when Thorne learns from crooked Detective Arnold Flass, who hates Napier, that Napier has been sleeping with Harleen Quinzel, a pop psychologist and Thorne's mistress. Thorne then sends Red Hood One and the Red Hood gang to Ace Chemicals to seize evidence that ties the plant to Thorne's empire before the GCPD could get their hands on them. In reality, Thorne already had the evidence cleared out and set Napier up to be gunned down by Flass and the GCPD. Bruce learns of the Red Hood gang cleaning out Ace Chemicals after overhearing Ethan informing Gordon and Commissioner Loeb about it. Bruce, Loeb, Alfred, Gordon, Lucius, and the Kanes were unaware of this, but Napier blackmailed Phillip into joining his gang. During the raid, Philip, who was blackmailed into joining the gang, tries to shoot Red Hood One, but misses. Red Hood One shoots and kills Philip. Gordon and Loeb arrive with the Strike Force intending to bring Red Hood One alive. Batman tries to capture Red Hood One, but the masked criminal escapes by jumping into a vat of chemicals.
- Around that time, Catherine and Commissioner Loeb aren't too fond of Batman due to being a vigilante and so Loeb sends the entire GCPD after the vigilante. Gordon begins to trust the vigilante and his motives which leads to Gordon working with him behind Loeb's back.
- Bruce meets a woman named Andrea Beaumont. Bruce and Andrea begin a relationship that hits Gotham's gossip columns. Bruce meets with Carl Beaumont, Andrea's father, who takes a liking to him. Bruce contemplates giving up his plans to be a vigilante for Andrea, ultimately though, Carl forces Andrea to break off her relationship with Bruce and they head to Europe together.
- Edward Nygma, as the Riddler, shuts off the power in Gotham, challenging Batman to turn it back on. Soon, the police find a body with its bones twisted and grown out of its skin. Batman finds out a scientist working with Lucius Fox had created a program that had similar effects. Bruce goes to visit Fox, but Fox stabs Bruce with the toxin, stating that the program was also his, and that Doctor Death is coming. Bruce wakes to seeing Fox being attacked by Doctor Death. Bruce stops him with the help of Gordon and Fox informs him that the substance he injected him with earlier was an experimental antidote for Dr. Death's bone toxin. However, the fight with Doctor Death puts Bruce in the hospital. Bruce is confronted by Gordon at the hospital, but Bruce feels he cannot trust him. Bruce as Batman searches for Dr. Death's next victim, but is too late, as Doctor Death had already reached them. The police corner Batman and open fire, mistakenly believing that he is the murderer. Batman is badly wounded, but Gordon helps him escape. Gordon and Batman then begin a tenuous partnership. Batman then goes to Gotham's catacombs, a popular tourist attraction, to find Doctor Death and the Riddler, having deduced that the two criminals are working together. Doctor Death and the Riddler then flood the catacombs. Batman uses his Bat blimp to stop the Riddler's airship and bomb. Batman arrives at his airship and tries to use a jammer device to stop the bomb. As his blimp explodes, Batman jumps onto the airship, where Doctor Death is waiting to fight him. Gordon arrives at Wayne Tower only to find the Riddler there, and falls into one of his traps. Doctor Death and Batman fight briefly, but the villain drops the jammer off the airship. After subduing Doctor Death, Batman sets off a bomb that destroys the inside of the airship; Dr. Death is killed in the explosion. The police then turn the power back on, only to find out the Riddler still has the power to flood the city by blowing up the reservoir. Batman destroys the airship, but fails to stop the Riddler from flooding the city.
- Bruce is rescued by a young Dick Grayson, who has been living on the streets since his parents died. Dick informs Bruce that the Riddler has taken control of Gotham. Alfred tells Batman to return to Wayne Manor through the secret entrance in the now dilapidated Crime Alley, the site of his parents' murder. Meanwhile, the military sends special forces soldiers to Gotham to help Gordon restore the peace. The Riddler uses a jumbotron every day to tell the people of Gotham that all he wants is a worthy opponent. The Riddler spots Gordon and the men on the rooftop, sending drones to stop him. The Riddler tries to destroy the building, but Batman stops him. Batman, Gordon, Fox and the soldiers plan a way to stop the Riddler. The next day, the Riddler appears on screen again to say that he will dedicate this "Zero Year" to the people of Gotham. Batman in a new costume comes driving in on a motorcycle and accepts the Riddler's challenge in order to buy time so Fox can discover their location. The Riddler drops Batman into a pit of lions. Batman fights and tames the lions, allowing Fox to find the Riddler's hiding place. Batman, Gordon and Fox try to attack the Riddler, only to fall into a trap. Fox is injured, but Batman saves him. The soldiers call in an airstrike to level Gotham while Batman finds the Riddler, as they play his last game. The Riddler challenges Batman to solve his riddles, allowing him one step closer to him on every answer he gets right. Gordon and Fox find a way to stop the jets from destroying Gotham. Batman grabs the Riddler, stopping his game. Gordon creates a Bat signal and successfully stops the jets. The Riddler reveals that to save Gotham, Batman must use his heart to turn the city's power back on; he must attach himself to an electrode. Batman successfully turns Gotham's power back on with the force of his own pulse.
- Jack Napier returns, now with his skin bleached as white, hair green, and having a permanent grin on his face after a botched surgical attempt by Matthew Thorne, Rupert's villainous twin brother. Getting angry at Thorne and now calling himself the Joker, Napier gets his revenge by killing Thorne in his penthouse after showing off his new look to him. As for Harleen, she becomes the villainous Harley Quinn with clown makeup and gets tortured to insanity by Joker through electric shock therapy.
- After taking control of Thorne's empire, Joker has Tony Falco get involved with Dr. Jonathan Crane and Ra's al Ghul, smuggling a fear toxin into Gotham inside toy rabbits. As a form of payment, Crane, who runs Arkham Asylum, diagnoses Falco henchmen as insane when they are captured so they can avoid prison. Wayne, who by now has become the vigilante known as Batman, discovers and foils the plan and knocks Falco out, leaving him tied to a searchlight for the police to find. The trussed-up mobster, covered in a tattered overcoat, projects a bat-like shape into the sky; this impromptu calling card would later evolve into the Bat-Signal. Batman also gives Catherine evidence of Falco's crimes and blackmails Faden into refusing Thorne's attempts at bribery and rendering an unbiased verdict, ensuring Thorne would finally be brought to justice. While imprisoned, Falco tries to blackmail Crane into letting him in on his plans with Ra's al Ghul. Crane instead wears his terrifying Scarecrow mask and uses his toxins on Falco, literally terrifying the crime lord out of his mind. Thorne is institutionalized in Arkham Asylum, continuously muttering the word "Scarecrow".
- Jonathan Crane (the Scarecrow) uses a tear toxin on his patients and dumping it into the water supply. He infects Catherine with it and Gordon allows Batman to take Catherine to the Batcave to escape Commissioner Loeb and his men when they try to catch him. Bruce is able to administer the antidote to Catherine just in time. He gives her two vials, one for mass production and the other for Gordon. Bruce though Scarecrow was working on his own, but then realizes he was working for Ra's. Ra's crashes Bruce's birthday party. Ra's explains that Scarecrow took the toxin from the blue flowers near his lair and was able to weaponize it and make people see their worst fears. Ra's master plan was to destroy Gotham with biological warfare and make the citizens kill each other out of fear. Ra's then went on and said that the League of Shadows have been around for centuries and were behind historical ecological disasters including the sacking of Rome, the Bubonic Plague, and the London Fire; and they believed what they did for the sake of the environment. Ra's then knocks out Bruce and sets Wayne Manor on fire.
- Bruce, Alfred, Lucius, Gordon, and Catherine work together to prevent Ra's from using a microwave emitter stolen from Queen Consolidated to disperse the fear toxin on the entire city through a monorail set to crash at Wayne Tower. Batman gives Lieutenant Gordon the Batmobile while he got on the monorail and took on Ra's. Ra's got an advantage as Bruce fought the same way, but Batman gets the upper hand. Gordon destroys the monorail track, and Batman stops the train. After knocking Ra's out, Bruce sends Ra's to Arkham Asylum. To prevent Ra's from revealing his identity, Batman comes up with the false identity of "Terry Gene Kase", and plants it along with credible photos, medical records, and police records for both Blackgate Penitentiary and Arkham Asylum. Batman takes an unconscious Ra's directly to Arkham where it is believed he really is the prisoner "Terry Gene Kase", a criminal with multiple personality disorder who has just been transferred to Arkham to finish out multiple life sentences. Along with attaching false information and a false identity to Ra's al Ghul's file, Batman attaches a false prescription of potent medication that ensures slurred speech and next to zero mobility. Arkham starts to believe that Ra's has multiple personality disorder. His files say he's claimed to be Black Lightning, Jesus, and even the "billionaire leader of a cabal of international assassins".
- Catherine does learn Bruce is Batman after Batman saves her and a boy she was protection from harm. Catherine starts to respect Bruce but he looses her love as Catherine believes there cannot be any room for her with Bruce Wayne and Batman. Catherine even urges Bruce to continue fighting crime and she promises to not tell anyone about his alter-ego, especially Ethan.
- James Gordon assigns Ethan Bennett and Ellen Yin to investigate the murder of Sal Maroni, who was found burned to death in Arkham Asylum, where Hugo Strange has taken over from Jonathan Crane. Yin looks at Batman in disgust for being a vigilante while Bennett believes that Batman is doing good. Yin and Bennett eventually discover that Maroni's killer is Maroni's own son Pino. Admitting to the crime, Pino said that Maronii had been trying to contact him for weeks to convince him to quit working at Arkham Asylum because of Hugo Strange being involved in shady dealings. Pino disagreed believing Strange was trying to make scientific breakthroughs. After finding out that Commissioner Loeb was getting suspicious of Strange, Maroni went to Pino as he was packing the shipments of chemicals and tried to get him to leave. Knowing that he could not overpower his father, Pino agreed, even suggesting to blow up the drug packages. Maroni agreed so Pino made a Molotov cocktail and threw it at his father. Dent and Catherine are able to get Pino a life sentence for the murder while suspicions on Hugo Strange continue to grow.
- Mayor Wilson Klass shares Sergeant Maxwell Cort and Detective Yin's disgust for Batman. Professor Strange accurately theorizes that Batman must be motivated by a traumatic loss wrought by violent crime, but goes on to claim that Batman's costumed vigilantism is primarily an exercise in power and control for his own benefit, rather than anyone else's. Gordon rebukes Strange's analysis, explaining that the costume is simply to scare criminals and Batman is honestly trying to help Gotham. But Mayor Klass sides with Strange and takes a hard stance against Batman, announcing on-air that he's forming a police task force to apprehend Batman and assigning Gordon to head it. Strange becomes a police consultant working alongside Klass and Klass grants Strange's request to have access to all police records,beginning with notable murder cases in Gotham, so he can start profiling the caped crusader and unravel his true identity. Gordon secretly withdraws all complete police records from Strange and recruits Cort instead of Yin believing that Cort is ill-equipped to keep up with Batman. Cort's obsession with Batman is so tense that he recruits Yin and a band of like-minded officers to join him on the task force, without Gordon's permission. Cort and his men find Batman at The Fish's hideout, in the midst of apprehending the drug peddler. They immediately open fire on Batman, causing him to flee and letting The Fish escape. Strange is also revealed to have an unhealthy obsession with Batman as Strange is jealous of Batman for the power and freedom he wields.
- Catherine and Gordon work to improve Batman's relationship with the public so Mayor Klass would reconsider his stance. Mayor Klass gets Catherine to go on a date with Strange. When Catherine ends the date because of Strange's endless ranting about Batman, he snaps and threatens her. At home, Strange calls Cort over to discuss their plans and Cort agrees to let Strange hypnotize him, under the pretense of alleviating stress. In reality, Strange use hypnosis to make Cort believe that he can be like Batman, but "better", thus turning Cort into the Night Scourge and making Strange publicly denounce Night Scourge's violent exploits as a result of Batman's existence. Cort himself is pleased with his work, believing that it proves he is just as 'good' as Batman, but admits he will need to face Batman to prove that he is better.
- Bruce, Lucius, and Alfred head to Metropolis after discovering Fish was working for Bruno Mannheim. Unknown to Bruce, reporter Clark Kent has no fondness for Batman since he believes Batman is brutal. Although Perry assigns Clark a sports story in Gotham City, Clark decides to investigate Batman. Through Mannheim's manipulations, Bruce starts dreaming of Superman in an alternate universe going rogue and taking over the world. Because of this, Batman breaks into the DEO and steals kryptonite. He builds a powered exoskeleton, a kryptonite grenade launcher, and a kryptonite-tipped spear in preparation for battling Superman. Mannheim lures Superman out of exile by kidnapping Lois and Martha Kent, Clark's adoptive mother. He pushes Lois off the LexCorp building. Superman saves her and confronts Mannheim, who reveals he manipulated him and Batman by fueling their distrust. Luthor demands he kill Batman in exchange for Martha's life. Superman tries to explain this to Batman, who instead attacks him and eventually subdues him using a kryptonite gas following a lengthy duel. As Batman prepares to move in for the kill using the spear, Superman pleads with him to "save Martha" - the same name as Batman's mother. Batman hesitates, yelling "why did you say that name?" until Lois arrives and explains what Superman meant. Coming to his senses about how far he has fallen from grace, he promises to rescue Martha. Superman regains his strength and goes after Mannheim, finally defeating him. Clark finally starts to trust Bruce right after he saves Martha from Mannheim's thugs. Out of concern he could go rouge and still distrusting the Government, Clark agrees to let Batman keep the shard of kryptonite. Even Lucius Fox starts to become fascinated with the kryptonite.
- Believing Catherine was in love with Batman, Strange gets Cort to break into Mayor Klass's home and assaults him and Catherine while dressed as Batman. Pretending to be Batman, Cort taunts the Mayor and kidnaps his daughter, threatening to kill her if he doesn't disband the task force. The next day, Mayor Klass institutes a 'shoot to kill' order against Batman and demands Catherine's safe return within five days or Gordon will be fired from the police force. Bruce, Alfred, Lucius, Clark, Lois, and Martha all know Batman wasn't behind Catherine's abduction since Batman was in Metropolis the night Catherine was kidnapped from her home in Gotham.
- Bruce tries to rescue Catherine the first time only to fail when Strange doses him with a specialized hallucinogen. After escaping from a mob of angry citizens with aid from street orphan Dick Grayson, Bruce enlists help from Gordon and Ethan to rescue Catherine. Leaving in his newly assembled Batmobile, Batman goes to Strange's penthouse and finds him once again dressed in a Batman costume and conversing with a mannequin. Batman appeals to Strange's ego and lets him gloat about staging the frame-up. But when Strange turns the subject towards Batman's true identity, Batman simply plays ignorant to Strange's ravings, saying he has no idea what Strange is talking about, and points out the Doctor's erratic and bizarre behavior as evidence that it is he who is mad and his profiling work is based on delusion. Gordon and Ethan then burst through Strange's door and Batman reveals that he has been recording their entire meeting, including Strange's confession to the kidnapping. Ethan finds Catherine tied up in another room, but otherwise unharmed. When Gordon attempts to arrest Strange, the doctor runs outside and finds himself in front of more cops. Mistaking him for Batman because of his costume, they act on Mayor Klass's shoot-to-kill orders, and open fire. Strange is hit numerous times before falling into a river. Presuming Strange to be dead, Batman goes in search of Night Scourge, who he now knows is Max Cort. Eventually, Batman defeats Cort with aid from Gordon and the GCPD.
- Gordon explains to Mayor Klass how Strange and Cort were responsible for kidnapping his daughter and it was the Batman who saved her. Grateful, Klass disbands the anti-Batman task force so the police can concentrate on the “real criminals” (much to the dismay of Yin and Loeb). Gordon meets with Batman one more time to inform him that Strange's body has still not been found. Gordon also adds that while the mayor and public have mostly forgiven Batman, there will always be people who resent and demonize him in some way because of what he does; but either way, Gordon believes that Gotham needs Batman so he will continue to work with him. Batman also grows to accept from Alfred that he is not insane and that being Batman is an act of sanity and order that defies the madness and chaos represented by crime and injustice.
- On a snowy Christmas Eve, a mysterious crime lord called Red Hood puts out a $60 million dollar bounty placed on Batman's head which leads to Batman being hunted by Floyd Lawton, Lester Buchinsky, Bane, Killer Croc, and Lady Shiva for the money. Bruce is also at a conflict with Dick who wants to go out onto the field only for Bruce to refuse because of the hit. Bruce, Lucius, and Alfred all begin to suspect that Red Hood is Victoria Beaumont, the mother of Andrea Beaumont, Bruce's former fiance. Batman breaks into Beaumont' penthouse to investigate only to find Beaumont' moll Tiffany Ambrose dead. Needing more information to solve the case, Batman breaks into the GCPD to access its national criminal database. While escaping, he encounters the corrupt SWAT team led by Howard Brandon, who all hope to collect the bounty money for themselves. Following advice from Gordon's daughter Barbara, Batman enters the sewers beneath the GCPD for permanent access to the database and finds Red Hood's crew planting explosives. Using the database, Batman deduces that Red Hood was kidnapped by the Jack Napier, presumably to access the Gotham Merchants Bank. At the bank, Red Hood removes his disguise for Batman and reveals himself as Napier, calling himself the Joker and confirming that Beaumont's husband Carl was engaged in shady dealings with Thorne before Napier took over. Joker even used Beaumont' money to impose the bounty on Batman. Batman chases the Joker to the Beaumont Steel Mill, where he frees Beaumont and defeats the poisonous assassin Copperhead.
- Commissioner Loeb is kidnapped by "Red Hood" since Loeb has refused to be corrupted and join Red Hood's organization. A protesting Loeb was then thrown into the prison's gas chamber, where he died from the poisonous fumes. Loeb's death has Klass put Gordon in charge of the GCPD, and the GCPD were shocked over what happened to Loeb at Blackgate. In reality, Loeb had actually been killed by the Joker, who had taken over Red Hood's operations earlier and posed as the fallen crime lord.
- Tracking the Joker to the Gotham Royal Hotel, Batman discovers that the villain and his men have filled the hotel with explosives, murdered the staff, and taken the guests hostage. The Joker berates the assassins for their failure to kill Batman, throwing Electrocutioner out a window to his death: Batman recovers his electric gloves. The assassins leave, except for Bane, who thinks Batman is coming for the Joker. After traversing the building, Batman finds the Joker on the roof but is forced to battle Bane. Thinking Batman is outmatched, Alfred alerts the police so they will intervene. As Bane escapes by helicopter, he fires a rocket at the Joker, who is thrown from the hotel by the concussive force. Batman saves the Joker, leaving him with the police. Puzzled by the events, the Joker is imprisoned in Blackgate under the care of Harleen; he tells Quinzel that he and Batman were destined to meet. The mob bosses all turn their backs on Napier due to viewing him as a loser and no longer wanted him to lead Rupert Thorne's criminal empire.
- On January 26, 2003, Jacob invites Bruce to a Bat Mitzvah to celebrate the 13th birthday of Beth and Kate. Bruce is unable to make it since the Joker broke out of Blackgate with Harley. But nevertheless, Bruce still sends along some presents over to them. After the party is over, Gabi decides to drive Beth and Kate home. After Jacob left, Gabi personally gifted Beth and Kate necklaces adorned with garnets, their birthstones, to symbolically represent the women they would become. She wanted the twins to stay connected to her, showing how her earrings matched their pendants. Beth and Kate happily accepted the gifts before embracing their mother. While returning home with Gabi, Beth and Kate posed for a polaroid picture with their necklaces to remember the day. Joker and Harley hijacked a school bus full of children while trying to get revenge on Batman for costing them Thorne's empire. Suddenly, the Joker uses the school bus to slam onto the back of the family's car and knocks them off a bridge. Batman tries to save his family by firing his grappling hooks. Beth urges Kate to escape out the rear window while she tries in vain to rouse an unconscious Gabi. As Batman goes to follow the Joker, Kate yells for Beth to get out of the car and grab her hand. Just as Beth reaches the window however, the car broke off from the grappling hooks and she cries out for Kate while falling into the river. Batman was able to save all the children on the school bus that Joker and Harley Quinn kidnapped, but was haunted by the fact that he failed to save his aunt and cousin. Bruce and Lucius both start spending hours pouring over what went wrong. Bruce, Catherine, Ethan, Dick, Alfred, Julia, the Fox family, and Gordon assist Kate and Jacob in searching for Gabi and Beth's bodies. Bruce was only able to find his aunt's. Bruce was deeply hurt when Kate started thinking that Batman was more concerned about catching criminals than saving lives since Kate felt Batman should've stayed to help and also when Jacob started blaming Batman for all of Gotham's problems, believing that Batman invited criminals into Gotham. Alfred urged Bruce to become closer to Kate and Jacob. But Bruce never told them of his secret identity.
- Dick learns that Tony Zucco, the man who murdered the Flying Graysons, his parents, is going to be released in exchange for helping the FBI with their case against the mafia in Gotham. When Special Agent Parker and the FBI makes a request to Mayor Klass to have Zucco be in their custody, Klass and the city officials debate whether they should release Zucco by discussing Dick and Zucco's childhoods. Alfred, Catherine Klass, and Jacob make an appeal to Mayor Klass, District Attorney Dent, and the cityl officials to not release Zucco because of what he did to Dick with Catherine having regrets on Malone. The FBI was unaware of this, but Zocco had a ledger containing incriminating information about the Mafia's operations in Gotham and Zucco was planning to escape the prison to retrieve the journal so he can blackmail the mob bosses into appointing him their leader, especially after Zucco snitches on Falcone to the Bureau. Despite Alfred's attempts to stop him, Dick races to Blackgate to confront his parents' killer. However as he steps out of the prison, Zucco is gunned down by a helicopter hired by a rival crime boss. While Zucco's death gives Dick some closure, his already-strained relationship with Batman becomes further complicated. When Dick presses him, Batman insists he knows nothing about Zucco's murder. Dick wants to go out onto the field but Batman refuses because of what happened to Beth.
- During the search for Beth, Jacob meets with a woman named Catherine Hamilton, the head of Hamilton Dynamics. Hamilton hires a team ov investigators to search for Beth. Knowing that Kate wasn't eating and sleeping, Hamilton decides to kill a deer and bribe a coroner in the GCPD to say that those fragments belonged to Beth, believing that Kate and Jacob will move on if they learn Beth is dead. Bruce, who thought Hamilton had no reason to lie, became devastated when he learned that his cousin died as well as Kate and Jacob. Jacob soon becomes an alcoholic and Bruce has to look after Kate while Jacob goes to rehab for what happened. Dick then understands why Bruce doesn't want him going out on the field.
- As time went by, Bruce and Lucius begin to notice the power grabs by the Bumper Mechanics engineering and toy company leader Oswald Cobblepot into many of Gotham's commercial and industrial districts and Bruce decides to move himself as a competitor in Cobblepot's bid to run the city. Cobblepot had sneaky dealings of his own, he murdered his partner Fred Atkins and put his hand in the toilet, hiding all the evidence. Later, he would inform the public that Fred was on extended vacation. Not only that, Cobblepot would scheme to build a supposed "Power Plant" for Gotham City's future. Standing in Cobblepot's way, however, is Mayor Wilson Klass, who believes the plant is unnecessary and is trying to bring down Cobblepot with aid from Dent and Catherine.
- A man named Waylon, alias Killer Croc, leads the Lucifer St. Gaston Circus Gang. Killer Croc kidnaps Cobblepot and blackmails him for help in returning to the surface. Cobblepot agrees to it when Killer Croc has evidence of Cobblepot's past crimes. Cobblepot agreed to help Killer Croc, but made it clear he wanted something in return, to which Killer Croc agreed to such a deal. Killer Croc made fun of Cobblepot's nose and the fact that Cobblepot carried an umbrella on him quite frequently, so Killer Croc decided to give Cobblepot a code name in their operation: the Penguin. Killer Croc was unaware of this, but Penguin is his birth father. A long time ago, Penguin and an unnamed woman gave birth to Waylon except that Waylon was born to resemble a crocodile. Getting disgusted by his son's appearance, Penguin locked him in a cage and finally made up his mind to abandon Waylon right after Waylon eats Hermione, Penguin canary. Penguin schemed to dump baby Waylon into the sewers and murdered the unnamed woman when she objected to Penguin murdering their son. Penguin succeeded in dumping Waylon into the sewers, met another woman, and fathered another son named Charles 'Chip' Cobblepot.
- Cobblepot uses Killer Croc's leadership over the Lucifer St. Gaston Circus Gang to 'rescue' Mayor Klass' baby nephew. Not only that, Cobblepot also has Killer Croc set up a crime wave all over Gotham and uses this as an excuse to run against Klass for mayor. Killer Croc kidnaps the Ice Princess and leaves behind a Batarang to fool the public into blaming Batman for it. When the GCPD try to arrest Batman, Catherine, who is unconvinced, has Batman take her hostage. Once Batman and Catherine escapes into the Batmobile, Cobblepot takes control of the vehicle and programs the vehicle to cause massive property damage all over Gotham and endanger civilians. Batman is able to regain control of the Batmobile, but his reputation is tarnished. Despite the best efforts of Alfred, Catherine, Dick, and Lucius, Bruce looses faith in Gotham when he learns that Cobblepot is sworn in as the new mayor.
- Around that time, Bruce Wayne is dating Selina Kyle, Cobblepot's secretary who is scheming to kill Cobblepot. Selina was once a dominatrix for the pimp Stan to survive and also sheltered a child prostitute named Holly working for him. Selina has a vendetta against Cobblepot for killing his parents, who objected to Cobblepot's crimes. When she is 13 years old, Selina discovers that the detention center's administrator has been embezzling funds, and she confronts her. In an attempt to cover up her crime, the administrator puts Selina in a bag and drops her in a river to drown (like a cat). She escapes and returns to the orphanage, where she steals documents exposing the administrator's corruption. She uses these to blackmail the administrator into erasing "Selina Kyle" from the city's records, then steals the administrator's diamond necklace and escapes from the orphanage. Selina eventually finds herself in "Alleytown – a network of cobblestone streets that form a small borough between the East End and Old Gotham." Selina is taken in by Mama Fortuna, the elderly leader of a gang of young thieves, and is taught how to steal. Fortuna treats her students like slaves, keeping their earnings for herself. Selina eventually runs away and starts working for Stan in order to survive.
- During Cobblepot's time as mayor, he decides to cut ties with Killer Croc knowing that he has no need for him anymore. So Cobblepot informs the corrupt GCPD of Killer Croc's hideout in the tunnels below "Hell's Point" and sends them there to kill him. Killer Croc is enraged to find humans in his home and kills all of them while setting fire to his own home in an animalistic fury. Enraged at Cobblepot's betrayal, Killer Croc has the Lucifer St. Gaston circus gang kidnap many of Gotham's first born children to drown them in toxic waste. Croc tries to kidnap Chip, but Cobblepot convinces Croc to take him instead. Although Batman is successful in saving the children and defeating the circus gang. Batman tries to talk Catwoman into sparing Cobblepot, but Catwoman refuses and electrocutes him to death. Killer Croc is injured due to accidentally bombing his own hideout when Croc sends his crocodiles equipped with missiles on Gotham. When Croc sent his crocodiles, Dick used a signal device to get the crocodiles to chase him back to the old Zoo, Croc's hideout. Killer Croc identifies Batman as Bruce Wayne when Bruce unmasked himself in front of Selina and Cobblepot in an effort to change Selina's mind about not killing. Killer Croc tries to kill Bruce only to die from his injures before Dick could intervene to protect Bruce.
- Bruce goes looking for Selina while having to deal with Cat Man, a serial killer preying on women due to issues he has with his mother. In the meantime, Chip blames Batman for his father's death while Batman is a fugitive from the law for what happened to the Ice Princess. When Gordon exonerates Batman of klling the Ice Princess due to finding Killer Croc's fingerprints on the batarang used to knock her out, Chip becomes enraged believing that Batman murdered his father and that Gordon covered it up. Chip kidnaps Barbara to lure Gordon over to him and tortures Gordon by beating Barbara in front of him. Batman intervenes with help from Catwoman and Dick. Chip is enraged to learn that Catwoman murdered his father and Batman makes a deal with Catwoman to leave Gotham or he will be after her for Cobblepot's murder.
- Dick develops feelings for Kate Kane only for Dick to cancel them out upon realizing that Kate is a lesbian. Kate comes out to Bruce, Catherne Klass, Alfred, Dick, Jacob, Catherine Hamilton, and Mary Hamilton that she is gay, which they are all accepting and in support of. Bruce starts to wonder if the rest of his living relatives would approve of him being Batman only for Jacob to hurt Bruce by blaming Batman for Chip's descent into madness as well as for all the madness in Gotham.
- The beginning of Dick Grayson's career as Robin, The Boy Wonder as Batman trains him in crime-fighting, against the judgment of Alfred. Robin proves to be a capable ally when he foils The Mad Hatter's plot to abduct and sell children into slavery. The story begins when the Mad Hatter is hired by Singh Manh Lee, the president of Rheelasia, to kidnap ten American girls for Lee's personal sex trafficking purposes. Batman and Robin are informed of the disappearances of eight girls by Captain Gordon and begin searching Gotham City for clues. After encountering difficulties in their search, Robin identifies one of the missing girls as Jennifer, a school acquaintance. While searching his school for leads at Batman's request, Robin discovers that the Mad Hatter is behind the kidnappings. Because Batman is aboard President Lee's yacht as Bruce Wayne, Robin decides to foil the Hatter's plot alone. Although Robin's efforts lead to the arrest of the Mad Hatter, the exploitation of President Lee, and the rescue of the captive girls, Batman is angered that Robin did not wait for his permission and assistance. Before Batman can reprimand Robin, Alfred intervenes and convinces him to commend his squire for a job well done. As Dick aids Bruce in his war on crime, Alfred fears that the boy may not be able to balance a normal teenage life with vigilantism.
- Bruce begins a relationship with a woman named Julie Madison, the daughter of Norman Madison, a failing businessman who borrows money from mobster Sofia Falcone. Catherine Klass was the one who shipped Bruce with Julie. Bruce Wayne loves Julie, but is reluctant to tell her the secret of his nighttime activities. However, Julie herself suspects that Bruce is hiding something from her.
- After borrowing money from Sofia, Strange sets up a private laboratory to test his theories. He then bribes a corrupt orderly to supply him with ideal test subjects: incurably insane inmates from Arkham Asylum who have been institutionalized for so long that they will not be missed. Strange's experiments have literally monstrous results, with his test subjects turning into gigantic, mindless "Monster Men", possessing superhuman strength and cannibalistic instincts. Strange uses the Monster Men to commit crimes so he can put together the money needed to pay back his Mafia connections. Batman becomes involved after discovering some of the gruesome remains of the Monster's Men's cannibalistic rampages. When Strange sets his creations free at an illegal poker game, helping himself to the victims' money after the slaughter, the Gotham mafia begins to grow suspicious. Batman tracks Strange down, but is captured by Sanjay and thrown to the Monster Men as an intended meal. Batman not only holds off the creatures, but uses them as part of an inventive escape. Strange is enthralled by Batman, believing that he has found a genetically perfect man. He creates one final Monster Man using a drop of Batman's blood, and while his creation still has many of the flaws of its "brothers", it lacks most of the grotesque disfigurements that had plagued Strange's earlier creations. Strange is subsequently forced to destroy his lab in order to evade capture. Soon after, he turns the Monster Men loose, including Sanjay's brother (who had also been mutated as a result of Strange's "treatments"), at Falcone's private estate in a bid to wipe out the mob's leaders, erasing his debt and covering up their ties to his work. In the battle that follows, all of the Monster Men are killed, along with Sanjay (who abandons Strange and dies trying to avenge his brother). Strange escapes amid the chaos.
- Batman and Robin engage in another encounter with the Monk, a man referred to as Niccolai and is the vampiric leader of a cult called The Brotherhood, based in an abandoned castle/manor house on the outskirts of Gotham City. His followers, among whom is the gothic Dala, feed upon the blood of captured victims. Only the most devoted acolytes are transformed into true creatures of the night however. Maintaining a link with the 1939 version, Julie Madison is once again turned into the Monk's pawn, as she is lured to the castle by Dala under the guise of the Monk being some sort of self-help guru. At present, the current origin of the character has not been revealed. It should be noted that Dala is not a vampire, but she hopes to become one so she can serve as Niccolai's right hand. In the end, Batman and Robin save Julie, but her father is executed by Sofia's thugs when Norman tries to kill Sofia to erase the debt. Distraught by her father's death, Julie leaves Bruce and Gotham and goes to Africa as a member of the UN Peace Corps.
- Strange mysteriously returns. He decides to work with another of Batman's enemies, the Scarecrow, and use him as a tool to help him capture Batman, while simultaneously having fallen into a further delusional state, as he engages in a "relationship" with a female mannequin dressed in Batman's cowl, reflecting his warped dual admiration and loathing of Batman. The Scarecrow turns on Strange when the professor's therapy proves effective enough to turn the Scarecrow against his "benefactor", tricking Strange into falling into the cellar of his mansion base where the twisted psychiatrist is impaled on a weather vane that the Scarecrow had left in the cellar earlier. The Scarecrow then uses Strange's mansion as a trap for Batman, but his attempt to use Strange's plan fails when he tries to use Crime Alley as the scene of a trap while ignorant of the reasons why that alley is so significant to Batman, with his "trap" merely consisting of luring Batman into the alley and decapitating a former classmate of Crane's in front of the hero. With Catwoman's help, Batman locates the Scarecrow's hideout and catches the Scarecrow in the cellar with Strange's body before the house is destroyed in a fire, but loses sight of Strange, with it being unclear whether Strange had actually survived the fall onto the weather vane - he claimed that he lured rats to himself by using his sweat so that he could eat them – or if the Scarecrow and Batman were hallucinating from exposure to Crane's new fear gas, although Batman concludes that the subsequent explosion of the house has definitely killed Strange
- A former LOA member named Bane starts developing ambitions to destroy Batman, whom he had seen train with Ra's al Ghul and Malcolm Merlyn. Aware that a direct assault on Batman would be foolish, Bane destroys the walls of Arkham Asylum, allowing its deranged inmates (including The Joker, Scarecrow, Riddler, Poison Ivy, Mad Hatter, The Ventriloquist, Firefly, The Cavalier, and Victor Zsasz, as well as minor villain, Film Freak, who Bane almost killed for spying on him afterward) to escape into Gotham City.
- Talia learns of Bane's ambitions and heads to Gotham to warn Batman. Talia provides Bruce with an ancient suit of armor known as the Suit of Sorrows that once belonged to the Order of The Pure, a splinter faction of the Order of St. Dumas, implying the two have a complicated relationship. According to the armor's legends, it can impart strength and speed of its wearer but also completely corrupt anyone whose heart and soul is not pure. At first, the Dark Knight was skeptical of the legend, but eventually exhibited aggressive behavior while wearing the Suit of Sorrows during patrols. Bruce later learned from a member of the Order of The Pure that the armor once belonged to a knight named Sir Geoffrey de Cantonna, who massacred hundreds of people in an alpine valley in 1190. Thus, the armor became one of the trophies displayed within the Batcave to remind Bruce that he must be ever vigilant not only in his crusade against crime, but also himself. Eventually, Bruce passed on the armor to a new vigilante, Jean Paul Valley, who was seemingly able to wear it without any side-effects. Bruce met Valley during his time outside of Gotham.
- After deciding against using the armor Talia gives him, Batman spends three months rounding them up. After the massive breakout at Arkham Asylum, Mayor Armand Krol made Gordon fully responsible for the consequences and gave him 24 hours to get the situation under control, otherwise he would call the National Guard, ending Gordon's career as a cop. However, that same night, Krol's home was invaded by Joker and Scarecrow, who used his fear toxin on Krol, making him afraid and forcing him to do as they commanded. They forced Krol to call the president of the union of firefighters to tell him that Krol was going to cut their rolls. Then, Joker and Scarecrow forced Krol to call the GCPD and give them false information that led them to a death trap set up by Joker. After learning of Batman's last encounter with Firefly, Joker decided to reveal the fact that they have abducted Krol and along with Scarecrow, they took Krol to the Gotham River Tunnel, where they forced Krol to call the National Guard; all with the intention of luring Batman into a trap. Krol was forced to call Gordon while still under the influence of the fear gas. The villains destroyed a wall of the tunnel, allowing the water to fill the whole place. Batman rescued an incapacitated Krol and as a result they were flooded with water inside the tunnel. Batman did his best effort, using every ounce of energy in him to get them both out of the death trap and after a long struggle, Batman saved them both. A few moments later, Krol was able to walk again and he moved on towards the edge of the river, where he was found by the GCPD and he was still in shock after witnessing Batman's determination. Because he was exhausted after saving Krol, Batman returns to Wayne Manor, where Bane awaits him. He fights Batman in the Batcave, defeats him, and delivers the coup de grâce: he breaks Batman's back and leaves him paraplegic, thereby having been the only man to have "Broken the Bat".
- While Bane establishes himself as ruler of Gotham's criminal underworld, Bruce Wayne passes the mantle of Batman to Jean-Paul Valley, also known as Azrael.
- Alfred summons Dr. Shondra Kinsolving to Wayne Manor to treat Bruce. Alfred asks Shondra to provide her expertise in medicine for Wayne's recovery. Wayne's butler Alfred Pennyworth told her that Bruce had been in a car crash, but Kinsolving knew it was a lie by examining the x-ray results. However, she decided to play along and tried her best to tend Wayne's wounds as she started to develop feelings for him. Unfortunately, she was kidnapped along with Lucius Fox, an event which Wayne helplessly witnessed. Lucius and Shondra were taken to the island of Santa Prisca, where they were held hostages until the Justice League Task Force found their location and their captors took them out of the island. Kinsolving soon learned that the responsible for her abduction was her brother Benjamin (now using the alias Benedict Asp), who wanted to use Kinsolving and her healing powers as part of an experiment for a new weapon he was developing. Asp took her and Lucius to his residence in England, where he started experimenting with them. Unfortunately, Kinsolving was unaware that her powers were being used to create a weapon of mass destruction. After a week of testing, Kinsolving was found by a still-injured Bruce Wayne in disguise and she denied knowing him. Asp however, knew that his mission was in peril and knocked Kinsolving unconscious, taking her away from England. Once they reached another safe haven, Asp experimented further with Kinsolving and as a test of the psionic weapon he developed, they murdered their adoptive mother from miles away. Asp kept her drugged and the constant exposure to drugs and mental strain caused her to become mentally unbalanced as she would switch from an adult mentality to a child-like mindset. When Bruce Wayne came to rescue her, Asp and Bruce struggled and Asp was injured in the fight. Kinsolving tried to heal her brother, but with her mind confused and in her drugged state, she killed him. Afterwards, she was filled with regret and used her powers to completely heal Bruce from his broken back. Unfortunately, the experience was too much for her mind and her psyche returned to that of a child permanently. Bruce Wayne bought a big residence, where Kinsolving could spend the rest of her days with the best medical treatment.
- Bane challenges Sofia by kidnapping the children of her capos. Under Batman's violent "persuasion", Sofia agreed to lay a trap for Bane, leading Batman and Robin to the exchange site designated by Bane's men. Though Batman's impatience soon turned the exchange into a deadly firefight, Sofia nonetheless recovered the children with the help of Robin, and was delivered to safety soon afterward. Bane would later succeed though in taking over Sofia's operation by shooting her in a head, putting her into a coma so he can takeover.
- As Batman, Jean-Paul grows increasingly violent, allowing the villain Abattoir to fall to his death. Jean-Paul also refuses to recognize Robin as his partner. Utilizing a sophisticated combat suit in place of the traditional Batman uniform, he fights and defeats Bane at the end, severing the tubes that pump the Venom into Bane's bloodstream, causing severe withdrawal. Valley then gives the weakened Bane a vicious beating, leaving him alive but broken. As a result of Batman's efforts to save his life, Krol started a campaign that would facilitate Batman's work outside of the law, unaware that by the time he changed his attitude towards Batman, there was another man wearing the cape and cowl. Krol commanded officer Kitch to not interfere whenever Batman was working on a case. Shortly after this, Batman started using extreme violence against criminals and Krol urged Commissioner Gordon to adopt such methods within the GCPD and to turn a blind eye on Batman's brutal methods. Eventually, James Gordon, who was once the Batman's largest supporter, now decried the actions of this new Batman and the bitterness between Krol and he intensified as the Mayor publicly endorsed Batman's methods.
- Dick Grayson has been blaming himself for Jean-Paul's behavior, as it had been he who had designed his original costume, which was very similar to a villain Bruce had recently defeated. That, combined with "the system", a kind of brainwashing Azrael had undergone, might have been the cause of his recklessness. Bruce tells him not to blame himself. Robin showed up when Bane and Jean Paul had their second sparring and managed to save the passengers of an elevated train while Az-Bats took down Bane. Much to Dick's relief, Jean Paul did not kill Bane and for a moment considered that perhaps Jean Paul was a worthy successor.
- Although Valley appeared to be doing a good job of cleaning up crime in Gotham, it was quickly brought to the attention of Bruce Wayne that his methods were both violent and irresponsible. However, he was also able to defeat Bane in single combat, albeit using the innovations of his new suit. Although Jean-Paul, in his mentally-altered state, believed himself to be a superior Batman, and a logical permanent successor, after Wayne's recovery, he was forcibly ejected from the position through physical combat when he refused to relinquish it. Feeling shamed, Valley returned to his identity as Azrael and sought to redeem himself in Batman's eyes.
- Jacob Kane begins to blame Batman for all of Gotham's and his family's problems. As a result, Jacob decides to form Crows Security. Jacob tried to ask Bruce for the money to start it, but Bruce refuses since he actually has respect for Batman. As a result, Jacob grows to look at Bruce in disgust. Jacob and Catherine Hamilton form the Crows on their own without Bruce's help. Gordon protests to having the Crows run around Gotham, but Krol enjoys the idea. Although Krol is willing to let the Crows work with the GCPD in law enforcement, he threatens to cancel the agreement with Jacob if Jacob and the Crows make a move against Batman, which Jacob reluctantly agrees to after insistence from Catherine Hamilton since Catherine believes they have to take small steps before eliminating Batman.