The pilot episode begins in the late 2010s in 2019. Batman, despite being in his late 50's, continues to fight crime in a new high-tech Batsuit. In the rescue of a kidnapped heiress, Batman suffers a mild heart attack and, at risk of being beaten to death by one of the kidnappers, is forced to betray a lifelong principle by threatening to use a gun. Ultimately, Bruce reluctantly decides that his time as Batman is over and vows "never again" as he shuts down the Batcave. By this time, his allies (Alfred Pennyworth, Commissioner James Gordon, Lucius Fox, Leslie Thompkins, Renee Montoya and Harvey Bullock) have either died of natural causes or retired. His partners Dick Grayson, Barbara Gordon, Selina Kyle and Tim Drake are still alive and have grown up and left or had falling-outs after their retirement from their alter-egos. All of his enemies (such as the Joker, Harley Quinn, the Penguin, Two-Face, the Scarecrow, Poison Ivy, the Riddler, Killer Croc, Deadshot, Clayface, the Mad Hatter, Mr. Freeze, Bane, Ra's al Ghul, Man-Bat, and Hugo Strange) are either retired, in prison, in exile, or dead, and he has severed his ties with Superman and the Justice League.

The story fast-forwards 20 years later to 2039 in Neo-Gotham, a futuristic megalopolis featuring staggering high rises and flying vehicles. Bruce is now an old man in his 70's and a recluse living in bitter isolation in Wayne Manor, with no companion but his guard dog Ace. Terry McGinnis is an athletic 16-year-old high school student and reformed troublemaker with a deeply ingrained sense of personal justice. Living on poor terms with his father Warren McGinnis, Terry disobeys his curfew one night to meet up with his girlfriend Dana Tan, only to incur the wrath of a group of the Jokerz gang harassing them. A high-speed motorcycle chase between Terry and the Jokerz leads them to the grounds of Wayne Manor, where they run into the elderly Bruce Wayne. Bruce and Terry fend off the Jokerz side-by-side, but the exertion aggravates Bruce's heart condition. Terry helps Bruce back to the manor and, while exploring the mansion, stumbles upon the entrance to the Batcave and thus discovers Bruce's secrets, only to be chased out by a recovered and angered Bruce.

Terry returns home to discover that his father has been murdered, apparently by the vengeful Jokerz. Soon after, though, he discovers that his father had stumbled onto information about the production of illegal chemical weapons by Derek Powers through Wayne-Powers (Wayne Enterprises now merged with Powers's company) and that the man actually responsible for his father's murder is Powers's personal assistant/bodyguard Mr. Fixx. Terry goes to Bruce for help but he refuses, feeling he is too old and too weak to be of any use and instead tells Terry to take the evidence to Barbara Gordon (who has become the new Police Commissioner). After the evidence of the illegal weapon production is forcibly taken from Terry by Derek Powers, Terry subsequently steals the Batsuit, intending to bring Powers to justice. Bruce initially opposes all of Terry's efforts and vehemently demands he return the suit but Terry convinces Bruce to let him take on the Batman mantle, partially by drawing on the fact they both lost a parent to criminals, and subsequently defeats Mr. Fixx. During the battle, Powers is exposed to the chemical and forced to flee into hiding to receive treatment which subsequently mutates him into a radiation-emitting entity, though he uses artificial skin to hide the accident. Realizing that crime and corruption are running rampant in Gotham without Batman's presence, Bruce offers Terry the chance to assume the role of Batman, with Bruce himself mentoring Terry and in addition to working as Bruce's chauffeur and assistant so that Terry can support his family.

The new Batman soon develops his own rogues gallery, with both new villains (the radiation-emitting metahuman Blight (a.k.a. Derek Powers); seductive shape-shifter Inque; hypnotist the Spellbinder; sound weaponizer Shriek; deadly assassin Curaré; insane eco-terrorist Mad Stan; cybernetically-enhanced African big game hunter the Stalker; nerdy psychokinetic Willie Watt and a new version of the Royal Flush Gang) as well as some of his mentor's old foes, such as a rejuvenated Mr. Freeze; Bane's strength-enhancing drug Venom reborn as slap-on patches; the longevous Ra's al Ghul; and somewhat inevitably, the Joker himself.

Terry also makes allies in Neo-Gotham, such as the 16-year-old computer genius Maxine "Max" Gibson. After discovering Batman's secret identity, Maxine helps Terry with everything from computer hacking to babysitting. Police Commissioner Barbara Gordon also works with Terry. Though initially unhappy about another person following in Bruce's dangerous footsteps, she admits that the city needs Batman, and that Terry could not be deterred from being Batman any more than she could have been from being Batgirl. He also has a relationship with Melanie Walker, who was forced to do the bidding of her family’s new Royal Flush Gang under the codename Ten. Terry and Melanie’s relationship is similar to that of Bruce and Selina Kyle.