In 1981 in Gotham City, a young Bruce Wayne runs away from his parents' funeral after they were killed, and falls into a pit where he is attacked by a swarm of bats, developing a fear for them. In present day, eighteen months after the battle between Superman and General Zod in Metropolis, Superman has become a controversial figure. Bruce is now a billionaire who has operated in Gotham City as the vigilante Batman for twenty years. Having witnessed the chaos of that battle in person, he sees Superman as an extraterrestrial threat to humanity.

After learning of Batman's form of justice, Clark Kent (Superman's civilian identity) seeks to expose him via Daily Planet articles. Wayne learns that Russian weapon trafficker Anatoli Knyazev has been contacting LexCorp mogul Lex Luthor. Meanwhile, Luthor attempts to persuade Senator June Finch to allow him to import kryptonite discovered after Zod's terraforming attempt, so that it can be used as a deterrent against future Kryptonian and metahuman threats. She declines, but Luthor makes alternative plans with Finch's subordinate, which grants him access to Zod's body and the Kryptonian scout ship.

Bruce attends a gala at LexCorp to steal encrypted data from the company's mainframe, but antiquities dealer Diana Prince takes it from him; she returns it after failing to access the information. While decrypting the drive, Bruce dreams of a post-apocalyptic world where he leads rebels against an evil Superman. He is awakened by an unidentified person, appearing through a portal, who tells him that Lois Lane "is the key" and urges him to find "the others" before vanishing. The decrypted drive reveals Luthor's files on several metahumans across the globe. One is Diana Prince, who appears in a photo from World War I. Wayne tells Alfred Pennyworth that he plans to steal the kryptonite and weaponize it, if necessary, to fight Superman.

A widely publicized congressional hearing, led by Finch, is held to question Superman's actions against Zod. A bomb smuggled in by Luthor via Wallace Keefe's wheelchair detonates, killing everyone present except Superman. Superman blames himself for not detecting it in time and self-imposes exile. Elsewhere, Batman breaks into LexCorp and steals the kryptonite. He builds a powered exoskeleton, a kryptonite grenade launcher, and a kryptonite-tipped spear in preparation for battling Superman. Meanwhile, Luthor enters the Kryptonian ship and accesses a database of technology accumulated from over 100,000 worlds.

Luthor 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 Luthor, 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. 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 in confusion long enough for Lois to arrive and explain 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 confronts Luthor on the scout ship.

Luthor executes his backup plan, unleashing a monster genetically engineered from DNA from both Zod's body and his own. Diana arrives with her metahuman powers on display, and joins forces with Batman and Superman against the creature. Though outmatched, Superman realizes its vulnerability to kryptonite and retrieves the spear. He impales the creature with it, but in its dying moments, the creature kills Superman, who was weakened by kryptonite exposure.

Following Luthor's arrest, Batman confronts him in prison, warning him that he will always be watching. Luthor gloats that Superman's death has made the world vulnerable to powerful alien threats. A memorial is held for Superman in Metropolis. Clark is also declared dead, and Wayne and Prince both attend his funeral in Smallville. Martha gives Lois an envelope containing an engagement ring from Clark. Bruce tells Diana that he regrets having failed Superman in life. He asks her help to form a team of metahumans, starting with those named in Luthor's files, to protect the world in Superman's absence. After everyone leaves, the dirt atop Clark's coffin levitates.
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