Superman kills Doomsday by driving the Kryptonite spear through his heart. Doomsday kills Superman by stabbing him through the chest with a large bone protruding from his elbow.
Bruce asks Diana to help him find the other meta-humans. Lex Luthor goes to jail.
After the attacks in Metropolis, Bruce Wayne considers Superman and those like him a threat. Clark Kent is trying to balance being a superhero with his relationship with Lois Lane. Lex Luthor asks U.S. Senator Finch to allow him to import a large kryptonite sample found in the Indian Ocean, taken from the wreck of Zod's other world machine. Luthor plans to use the kryptonite to create a weapon to defeat Superman since it is a substance that he has found to weaken Kryptonian cells. Batman attempts to intercept Lex's illegal import of the kryptonite, but is stopped by Superman, who demands Batman cease and desist permanently. Lex stages two mass killings with Superman present to make him look responsible for the deaths, including a bombing at the U.S. Capitol during a hearing with Senator Finch present (Lex's assistant Mercy is killed as well). Batman tracks the kryptonite to the Kryptonian ship, where Lex has removed Zod's fingerprints in order to reactive the ship's chrysalis chamber. He cuts himself and drips his blood onto Zod's body as he lowers it into the module.
Knowing that Lex Luthor also has interest in protecting mankind from the "meta-humans" Bruce hacks Luthor's mainframe, but his drive is temporarily stolen by Diana Prince. When Bruce finds out that she gave it back, he notices that Luthor has been keeping tabs on her, Aquaman, Flash, and Cyborg. In a dream, he is encountered by the Flash (traveling through time) to tell him he was "right about him all along," leading Bruce to believe that he needs to stop Superman and kill him, so he steal the kryptonite from Lexcorp. Knowing Batman wants Superman dead, too, Luthor stages another elaborate kidnapping involving Lois. When Superman confronts Lex, he tells him that he needs to bring him the head of Batman or his mother will die (indicating that Lex knows both the secret identities of Superman and Batman). Superman flies to Gotham City, where he and Batman fight. As Batman wins and is about to kill Superman, Superman says "Martha will die." Batman hesitates since that was the name of his mother, and Lois intervenes and tells him that Martha is Clark's surrogate mother, causing Batman to realize Flash meant he was right all along about Lex being evil, not Superman. He tells Superman he will save his mother so Superman can deal with Lex.
Batman saves Martha Kent. When Superman returns to Lex empty handed and demanding Lex's submission to the authorities, Lex turns his attention to his creation, a mutant hybrid of Zod's Kryptonian and Lex's human DNA, Superman's Doomsday. As Doomsday is about to attack Lex, Superman stops it and takes the fight outside. Doomsday is able to absorb all energy used against it and becomes stronger with every attack. When Superman pushes him to the outer reaches of the stratosphere, the President orders the nuclear strike since Superman would be the only casualty. It hits them both, but Doomsday plummets back to Earth while Superman regains his strength from the sun.
Alone against Doomsday, Batman is saved by Wonder Woman, who gladly takes on Doomsday as Superman returns. They realize that the kryptonite spear is the only thing that will kill Doomsday, so Superman retrieves it and flies back to finish the job. While fighting Doomsday, Wonder Woman cuts off his right arm, but his mutant healing ability causes the arm to grow back as a large bony protrusion. Superman tells Lois he loves her and drives the spear through Doomsday's chest while Wonder Woman has him ensnared in her golden lasso. As he dies, Doomsday stabs Superman through the chest, killing him.
A funeral for Superman is held in Washington, D.C. while Clark Kent's body is laid to rest in Smallville. Martha presents Lois with a surprise that Clark wanted to give her, a wedding ring, which she puts on. Bruce and Diana agree to find the other meta-humans. Batman visits Lex in jail to tell him he will always be watched. Lex is unphased, since now that Superman is dead the extraterrestrial forces he really wants to combat will find their way to earth. Back in Smallville, Lois takes a handful of dirt and throws it on Clark's coffin.
Just before the credits, dirt on top of the coffin slowly begins to rise, indicating a heartbeat.