In 1981, Bruce Wayne witnesses his parents get killed by a mugger. During their funeral, he runs away and falls into a cave, where a circling vortex of bats inspires him. He eventually grows up to become the Batman, a vigilante dedicated to cleaning up the streets of Gotham City. When the Black Zero begins its attack on Earth, Bruce drives through the streets of Metropolis, narrowly avoiding the destruction. He manages to evacuate most the employees out of the Wayne Financial office building before Zod's heat vision goes ballistic and causes the structure to collapse, killing a board member named Jack. Bruce tries to help the civilians, saving a little girl and another employee whose legs were crushed by falling debris, all the while watching the battle between Superman and General Zod going on above.
Eighteen months after Superman's debut to the world, society is still reeling from the revelation of aliens existing and Superman himself has become a controversial figure. Bruce himself sees Superman as an existential threat to humanity and is determined to extinguish that threat at all costs despite the protests of his butler Alfred Pennyworth, who worries Bruce is going over the edge. As Bruce has spent almost twenty years fighting crime in Gotham, only to have little to show for his efforts, as well as seeing his sidekick Robin be murdered by the Joker, he's become increasingly bitter, burnt out, and paranoid, and Superman's appearance has only served to further that.
Lois arrives in the African country of Nairomi to interview a terrorist leader. Her photographer, James Olsen, turns out to be a CIA agent and he's shot and killed when he's discovered. Superman swoops in and saves her while downing a drone. As this happens, people under the employment of Lex Luthor burn some bodies. These deaths are blamed on Superman, with the media debating whether Superman must interfere in these affairs.
After learning of Batman's brutal form of justice (which involves branding certain criminals, leading to them being killed in prison), Clark Kent seeks to expose him via Daily Planet articles. He investigates around Gotham despite Perry's refusal to run anything about Batman. Wayne learns that Russian weapon trafficker Anatoli Knyazev has been contacting LexCorp CEO Lex Luthor. Luthor attempts to persuade Senator June Finch to allow him to import a mineral called kryptonite, irradiated pieces of Kryptonian minerals found in the Indian Ocean 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, granting 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 due to it having military grade encryption. While decrypting the drive, Bruce dreams of a post-apocalyptic world where he leads rebels against an evil Superman leading an army of parademons. 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, who appears in a photo from World War I. Another is a young man foiling a convenience store robbery using superhuman speed. The third clip contains footage of a man 20,000 feet under the sea destroying an underwater drone. The last one is of a young man whose mangled body becomes reconstructed with cybernetics from alien technology. Bruce tells Alfred that he plans to steal and weaponize the kryptonite, if necessary, to fight Superman.
A widely publicized congressional hearing, led by Finch, is held to question Superman's actions. A bomb smuggled in by Luthor detonates, killing everyone present except Superman. Superman blames himself for not detecting it in time and goes into self-imposed exile. Elsewhere, Batman breaks into LexCorp and steals the kryptonite. He builds a powered exoskeleton, a kryptonite grenade launcher, and a kryptonite-tipped spear. Meanwhile, Luthor enters the Kryptonian ship and accesses its vast database of technology.
Luthor lures Superman out of exile by kidnapping Lois and Martha. 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 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. Realizing to his horror that he nearly murdered an innocent man in cold blood and how far he has fallen from grace, Batman throws the spear aside and promises to rescue Martha. Superman regains his strength and confronts Luthor on the scout ship.
Luthor executes his backup plan, however, unleashing a monster genetically engineered from DNA from both Zod's body and his own; he calls it "Doomsday". Superman first tries to fly Doomsday up to space, where the President gives the order to launch a nuke at the monster. However, the beast only grows stronger. Diana then arrives wearing armor and wielding a sword and a shield, joining Batman and Superman in their fight against the creature; she manages to cut off its hand, but it only makes Doomsday angrier. Superman and Batman realize Doomsday can only be killed by kryptonite and so Lois retrieves the spear. Clark tells Lois he loves her and that she is his world. With Diana restraining Doomsday with her Lasso and Batman weakening it with a Kryptonite grenade, Superman flies in and fatally impales Doomsday in the chest with the spear. In its dying moments, Doomsday manages to get loose and impales Superman, who was weakened by kryptonite exposure, in the chest with a bony protrusion. They both collapse to the ground dead.
Following Luthor's arrest after Lois and the Daily Planet expose his crimes, Batman confronts him in prison. Luthor plans to invoke the insanity plea so he will be declared unfit stand trial, only for Batman to reveal that he's arranged for Luthor to be transferred to Arkham Asylum. Luthor cryptically warns that with Superman's death, "the bell has been rung" and that "demons" will be coming from the sky to bring the apocalypse to Earth. A memorial is held for Superman in Metropolis, his sacrifice being mourned the world over. Clark is also declared dead, and Bruce and Diana both attend his funeral in Smallville, with Bruce anonymously covering the costs. Martha gives Lois an envelope containing an engagement ring from Clark. Bruce tells Diana that he is determined to make things right and honor Superman's sacrifice. He asks her to help him form a team of metahumans, starting with those named in Luthor's files, to protect the world in Superman's absence. As they depart, the dirt atop Clark's coffin levitates.
