Eighteen months after the destructive battle in Metropolis (
Man of Steel),
Superman has become a controversial figure, incurring the wrath of billionaire
Bruce Wayne, who has covertly operated in
Gotham City as a vigilante referred to as Batman for nearly two decades and who blames Superman for the mass casualties that resulted from his fight with
General Zod. Superman, in his public identity as
Daily Planet journalist Clark Kent, in turn sees Batman as dangerous and seeks to expose him.
LexCorp's mogul
Lex Luthor also sees Superman as a threat and convinces Senator June Finch to help him recover
Kryptonite from Zod's failed
terraforming attempt from the
Indian Ocean. Finch later stonewalls Lex's efforts to use Zod's DNA and the Kryptonian scout ship recovered from the battle to create a biological weapon.
Wayne infiltrates a fundraiser promoted by Luthor to retrieve data from LexCorp's mainframe, but his drive is stolen by mysterious antiques dealer
Diana Prince, who learns that Luthor has files on herself,
Barry Allen,
Victor Stone and
Arthur Curry. Wayne later receives the drive back from her after she duplicates the files. He learns not only of Luthor's experiments with Kryptonite, but also his ongoing investigation about
metahumans including Prince herself, whom he learns is an immortal warrior. When having a nightmare in which Superman has turned the world into a dystopian society, Wayne is interrupted by the Flash, who has time traveled from the future to warn him of an impending threat. Batman attempts to retrieve the Luthor's Kryptonite, but is intercepted by Superman, who orders him to cease his activities. Later, Finch summons Superman to a Congressional hearing to debate the validity of his actions, where Luthor masterminds a bombing that kills dozens of people, including Finch. The public blames the bombing on Superman, who goes into self-imposed exile.
Batman retrieves the Kryptonite and prepares to launch a preemptive strike against Superman. Elsewhere, Luthor activates the Genesis Chamber aboard the scout ship and splices his own DNA and Zod's. Luthor endangers Superman's love interest
Lois Lane to lure him to LexCorp Tower, where he reveals that he has been aware of Superman's secrets for some time. Lex blackmails Superman into confronting Batman by holding his adoptive mother,
Martha Kent, hostage at an undisclosed location. Superman is unable to reason with Batman, leading to a vicious fight in which Batman nearly kills Superman with a Kryptonite spear. Thinking death is near, Superman pleads for Batman to "save Martha" which was also
the latter's late mother's name, causing him to come to his senses and realizes Superman is not a threat. Upon learning of Luthor's plan, Batman leaves to rescue Martha while Superman confronts Luthor, who unleashes a monstrous artificially bred
creature made from Zod's remains. Superman and Batman join forces to fight him and are aided by an arriving Prince in her Wonder Woman warrior attire, but are outmatched due to Doomsday's ability to absorb and redirect energy. Realizing that their shared Kryptonian DNA result in shared vulnerabilities, Superman retrieves the Kryptonite spear and sacrifices himself to impale Doomsday with it, while Doomsday stabs Superman with his bone protrusions.
Luthor is arrested after Lane exposes his numerous crimes; when he is visited by Batman in prison, he gloats that Superman's death has made Earth vulnerable to new threats from beyond Earth. A memorial is held for Superman in Metropolis, and as Clark is also declared dead, Wayne, Lane, Martha and Prince attend a private ceremony in
Smallville. Martha passes an envelope to Lois, which contains an engagement ring and thus revealing that Clark was planning to propose to Lois. After the funeral, Wayne reveals to Prince that he plans to
form a team from Luthor's file subjects to protect the world in Superman's absence. Later, a faint heartbeat begins echoing from Superman's grave and the dirt around it begins to levitate.