Plot

In a flashback to his childhood, Bruce Wayne runs from his parents' funeral. He falls into a cave, where a circling vortex of bats elevates him back to the surface. Bruce's mother Martha (Lauren Cohen) and Father Thomas (Jeffrey Dean Morgan) were killed in a street mugging in front of Bruce.

Eighteen months after his destructive battle with General Zod in Metropolis, Superman (Henry Cavill) has become a controversial figure. The fight between Superman and Zod killed thousands of people and Bruce himself was on ground and witnessed the human suffering caused by it. Bruce's own office building, along with its hundreds of employees were destroyed in the battle between Superman and Zod. Billionaire Bruce Wayne (Ben Affleck), who has operated in Gotham City as the vigilante Batman for nearly two decades, sees Superman as a potential threat to humanity.

Meanwhile, a group of freelance divers retrieve a huge chuck of Kryptonite from a location in the Indian Ocean. Lois Lane interviews General Amajagh (Sammi Rotibi) in Africa, but her cameraman Jimmy Olsen (Michael Cassidy) is executed when he is found in possession of a CIA tracking device. Anatoli Knyazev is Amajagh's head of security, who betrays Amajagh and kills all his men, and leaves before Superman arrives to save Lois. Superman is blamed for the deaths of the villagers, who were killed by Anatoli. Perry White (Laurence Fishburne) runs the Daily Planet newspaper and launches a media campaign against Superman.

The US Congress conducts inquiry into Superman's conduct and wanton acts of destruction, led by Senator Finch (Holly Hunter), who is horrified to hear from witnessed their stories of pain & loss directly caused by Superman's actions.

After learning of Batman's form of punishment (torture and branding), Clark Kent, Superman's alter-ego, seeks to expose Batman via Daily Planet articles. At this point both Superman and Batman consider each other to be a public nuisance who operate outside the ambit of law and cause more harm than good.

Wayne learns that Russian weapon trafficker Anatoli Knyazev (Callan Mulvey) has been contacting LexCorp mogul Lex Luthor (Jesse Eisenberg). He thinks it is because Luthor wants to bring a dirty nuclear explosive into Gotham city. Mote Bruce tracks Anatoli and makes a remote copy of his phone data when he meets Anatoli at a bar. Bruce finds that the phone was transmitting data into the personal servers of Lex Luthor.

Meanwhile, Luthor tries to persuade Senator June Finch to allow him to import Kryptonite retrieved from the Indian Ocean following Zod's Terraforming attempt, claiming he wants to maintain it as a "deterrent" against Kryptonians, but she denies the request. Luthor had performed experiments on Zod's body using a small Kryptonite sample and knew that Kryptonite causes severe degradation of cells in the bodies of Kryptonians.

Luthor also makes side dealings with Finch's subordinate and demands access to Zod's body and the Kryptonian scout ship. Luthor wanted to build a team of meta-humans (people with superpowers) as a deterrent to rouge superheroes.

Wayne attends Luthor's party at LexCorp, where he meets an antiques dealer named Diana Prince/Wonder Woman (Gal Gadot). Wayne plants a wireless device on Luthor's data servers and retrieves encrypted data from the company's mainframe. While Decrypting the drive at the Batcave, Wayne has a dream of a post-apocalyptic world, where he leads a group of rebels against Superman. He is snapped out of the dream by an unidentified being, seemingly talking to him from the future via a portal, who warns him of Lois Lane's (Amy Adams) crucial role in the distant future and urges him to find "the others" before vanishing.

Wayne later discovers that Luthor is not only experimenting with Kryptonite but also investigating meta-humans. The Decrypted drive reveals Luthor's files on several meta-humans across the globe. One is Diana, who appears in a photo from World War I. Wayne contemplates converting the Kryptonite into weapons to go to war with Superman. Wayne also finds that a large shipment of Kryptonite found in the Indian Ocean is now aboard a ship bound to be delivered to Luthor. Other people experimenting with Kryptonite is Prince herself, who is an immortal warrior. Wayne admits to Alfred Pennyworth/butler (Jeremy Irons) that he plans to steal the Kryptonite to convert it into a weapon, should it become necessary to fight Superman.

As Batman chases the consignment, he is confronted by Superman, who stops Batman. as a result, the Kryptonite reaches Luthor. However, Batman had a tracking beacon on the truck and know the location of the Kryptonite.

At a congressional hearing, as Finch questions Superman on the validity of his actions, a bomb planted by Luthor explodes, killing everyone present but Superman. Believing he should have detected the bomb, and frustrated by his failure to save the people, Superman goes into self-imposed exile. Batman breaks into LexCorp and steals the Kryptonite, planning to use it to battle Superman by building a powered exoskeleton, and creating a Kryptonite grenade launcher and a Kryptonite-tipped spear. Meanwhile, Luthor enters the Kryptonian ship and learns details of its alien technology & initiates the creation of a mutated being containing Kryptonian and human DNA.

Luthor kidnaps Martha Kent (Diane Lane), Clark's adoptive mother. He reveals that he has manipulated Superman and Batman by fueling their distrust for each other. He demands Superman kill Batman in exchange for Martha's life. Superman tries to reason with Batman, but Batman instigates a fight and ultimately subdues Superman. Before Batman can kill him with the spear, Superman urges Batman to "save Martha", whose name is also shared with Wayne's late mother. Lane arrives and explains the situation which convinces Batman that Superman is not a threat. Unwilling to let someone else's mother die, Batman leaves to rescue Martha, while Superman confronts Luthor on the scout ship.

Luthor executes his backup plan, unleashing a genetically-engineered monster with DNA from both Zod's body and his own. However, Prince arrives unexpectedly. Revealing her meta-human nature, she joins forces with Batman and Superman to fight the creature. They are soon outmatched by its power, as it can absorb and redirect energy. Realizing that it is vulnerable to Kryptonite, Superman retrieves the Kryptonite spear. With Batman and Prince's help containing it, Superman impales the monster. As it dies, the creature stabs and kills a weakened Superman with one of its bone protrusions.

Luthor is arrested, and Batman confronts him in prison, warning Luthor that he will always be watching him. Luthor gloats that Superman's death has made the world vulnerable to powerful alien threats, and that something bigger is coming to Earth. A memorial is held for Superman in Metropolis. Clark is also declared dead, and Wayne, Lane, Martha, and Prince attend a private funeral for him in Smallville. Martha gives an envelope to Lane which contains an engagement ring from Clark. After the funeral, Wayne reveals to Prince that he plans to form a team of meta-humans, starting with those from Luthor's files, to help protect the world in Superman's absence. After they leave, the dirt atop Clark's coffin begins to levitate.