Feigning remorse for his past, Joker, Michael Emerson convinces Bartholomew Wolper, Michael McKean, to invite him on a talk show to tell his story, even as he plots an escape with an old henchman who supplies him with mind-controlling lipstick. Meanwhile, Superman, Mark Valley, who operates as a government asset willing to quietly help people, is pressed by the President to put an end to Batman’s vigilante activities. Framing these actions is a deepening rift between the United States and the Soviet Union over the island of Corto Maltese. As Batman’s presence continues to humiliate the national authorities, Ellen Yindel, Maria Canals-Barrera rises to the role of commissioner and orders Batman’s arrest, while Superman warns that the government won’t tolerate him much longer.
Joker makes his talk show appearance on David Endocrine’s show, Conan O’Brien hosting the program, as Batman battles the GCPD on the studio roof; in the chaos, Joker murders Wolper, gasses the studio to death, and escapes. He then tracks Selina Kyle, Tress MacNeille, and uses one of her escorts along with his lipstick to seize control of a congressional representative who calls for a nuclear strike on the Soviets before dying. Batman’s investigation leads him to Selina, whom he finds bound and dressed as a certain icon of female empowerment. Carrie Kelley, Ariel Winter, notices cotton candy on the floor and realizes Joker is at the fairgrounds. Batman pursues the Joker as the henchman’s life is claimed, and the Joker’s indiscriminate gunfire rains down on bystanders.
As the confrontation peaks, Batman corners a wounded and partially blinded Joker. The Caped Crusader confesses feeling responsible for every murder Joker has committed and pledges to stop him once and for all. In the brutal exchange, Joker stabs Batman, and Batman breaks Joker’s neck in front of onlookers. Content that he has forced Batman into losing control and will be branded a murderer, the Joker twists his neck and dies. The GCPD arrives, Batman, bleeding heavily, fights his way to Kelley and escapes. After Superman deflects a Soviet nuclear missile, he is struck by the blast, and the detonation triggers an electromagnetic pulse that wipes out all electrical equipment in the United States and ushers in a nuclear winter.
As Gotham descends into chaos, Batman, Kelley, and Commissioner Gordon rally the Sons of Batman and the city’s citizens to restore order, while Yindel accepts that Batman has grown too powerful to be toppled. With the rest of the powerless U.S. laid waste by crime, Gotham becomes the safest city in America, a reality that unsettles the President and spurs a final move to stop Batman once and for all. Batman and Superman agree to meet in Crime Alley for a defining clash. Wearing a powerful exoskeleton and backed by Kelley and former hero Oliver Queen, Robin Atkin Downes as Green Arrow, Batman engages the Last Son of Krypton with a suite of tactics intended to tilt the battle in his favor. When Kryptonite dust fills Superman’s lungs, his powers fade, and Batman claims victory without killing him. The confrontation ends with what appears to be Batman’s death in the arms of Wayne Manor’s ruin, and Alfred Pennyworth, Michael Jackson, dying of a stroke beside the fallen estate.
In the aftermath, the world learns that Bruce was Batman; his secrets die with the manor and his finances vanish. As Superman departs Wayne’s funeral, he shares a knowing wink with Carrie Kelley after sensing a faint heartbeat coming from Bruce’s coffin. In the hidden depths beneath the earth, Bruce is revealed to have faked his death and to be plotting a quieter, more discreet continuation of his mission, now allied with Kelley, Queen, and a devoted network of followers.