Three years after the Battle of Metropolis, Clark Kent is protecting the world as Superman and working as a reporter for the Daily Planet newspaper. Superman has become a controversial figure, with some blaming him for the destruction caused by General Zod and others believing him to be a hero. Lois Lane is covering the civil war on Khandaq in the Middle East, while Clark is forced to cover minor stories. He befriends Jim Olsen, a photographer who lost his legs in Zod's invasion, but doesn't blame Superman, and applied for the Daily Planet because they defend Superman, and they cover a football game between Metropolis and Gotham City in which Clark meets Victor Stone, a quarterback for the Metropolis team whose father, Dr. Silas Stone, is an robotic engineer at S.T.A.R. Labs who spearheaded a new high-tech prosthesis program which includes Jim's legs.
Bruce Wayne was in Metropolis during Zod's invasion and believes Superman to be a threat, elaborating counter-measures to disable him if necessary. He's also funding an effort to rebuild a vacant area of Gotham with new housing projects for low-income families. As Batman, he's been active for 15 years, but remains a fugitive of justice that many believe to be an urban legend. Clark has been studying the Batman's sightings despite his editor, Perry White, not seeing any potential in that story.
Lex Luthor funded Metropolis' rebuilding after Zod's invasion and has been contracted by the United States government to reverse-engineer leftover Kryptonian technology for them. Luthor believes Superman to be a threat and runs a smear campaign against him through the media vehicles he owns, and is funding the development of anti-Superman weapons, including Kryptonite, which is created through exposure to energy from the World Engine. Luthor also has collected Zod's body and harvested his DNA, using technology based on the Genesis Chamber to craft a biotechnological weapon that could fight Superman.
Senator Veronica Cale is supervising Luthor's experiments, but believes the biotechnological weapon shouldn't be deployed due to potential backlash given many still regard Superman as a hero, something Luthor seeks to rectify.
Luthor has also been monitoring other individuals with super-humans powers umbeknowst to the government, and has captured and experimented on several of them through Cadmus, a LexCorp subsidiary dedicated on genetic research. A paramilitary team under LexCorp's employ, led by his head of security Anatoly Kniazev ambushes Aquaman after luring him into a trap in a LexCorp oil rig and captures him, bringing him to Cadmus for experimentation. Luthor's activities have attracted the attention of Diana, princess of Themyscira, who is on Men's World masquerading as a wealthy humanitarian. She connects Luthor to the string of disappearances she's been been investigating and decides to pursue that lead to Metropolis.
Clark calls Lois in Khandaq, which doesn't allow Superman in their airspace. The camp is attacked by rebels and Superman springs to action to help Lois and the soldiers, in the process causing an international incident. Lois returns to Metropolis, while Cale uses the incident to convince the American Congress that Superman represents a potential political liability if they continue to harbor him. Superman is later informed by General Swanwick, one of his fiercest supporters within the government, that the Congress has ordered him to attend a summit in Washington, D.C. to discuss his place in the world. The aftermath of Superman's actions in the Middle East are observed by Bruce, Diana and Luthor.
Bruce finds out about Luthor's research on anti-Superman weapons and travels to Metropolis with Alfred Pennyworth under the pretext of meeting Luthor to discuss a partnership to rebrand Gotham's impoverished neighborhoods in order to learn more. Bruce doesn't trust Luthor with alien technology as much as he doesn't trust Superman.
Luthor promotes a fundraiser for the Metropolis Museum, the building where Zod was murdered, something which he makes sure to point out. Clark, Lois and Jim are covering the event, with Bruce, Alfred, Diana, Kniazev and Luthor's private assistant Mercy Graves in attendance. Clark interviews Bruce and questions him about the Batman, Bruce dances and flirts with Diana, who also scans Kniazev. Bruce and Luthor have a brief argument in which Bruce plants a device in Luthor's phone, so he can steal the access passwords to LexCorp Tower and infiltrate it, using a signal jammer to evade security.
Batman steals data about Luthor's projects, but an algorithm projected by Luthor adapts to the jammer and alerts security. Batman evades Kniazev and his men, but is then confronted by Superman, who believes him to a criminal. Batman refuses to surrender and, after a brief confrontation, escapes from Superman in the Batmobile. Batman sightings in Metropolis are enough for Lois and Clark to convince Perry to let them go to Gotham for a more extensive investigation. Luthor later reviews footage of Superman and Batman's encounter acquired by the government's satellites and retrieves the signal jammer Batman left behind, which gives Luthor an idea.
Superman arrives at the summit, with the entire world watching. Senator Cale accuses him of being dangerous, and Superman defends himself and explains his ideals. The Congress pushes for Superman to swear allegiance to them, including disclosing secrets of his identity and upbringing, but Superman refuses, claiming he will not become a tool of the government.
Superman hears Batman's signal jammer and feels weak. He loses control of his powers and the building is evacuated just as it explodes, injuring several people and killing General Swanwick. Senator Cale accuses Superman of being the culprint, and he is forced to escape when the military intervene. Superman is declared a public enemy, while Luthor is informed that the Kryptonite has been a success.
Clark returns to the damaged building and locates Batman's signal jammer, and becomes convinced that Batman framed him and is indirectly responsible for General Swanwick's death. Superman returns to Metropolis in search of Batman, but Bruce manages to evade him. He learns about Kryptonite from Luthor's files and steals samples from it from a LexCorp outpost stationed in the Indian Ocean where the World Engine has first activated.
Meanwhile, Diana lures Kniazev and his men into a trap and confronts them. Kniazev escapes, but Diana manages to interrogate one of his soldiers, using the Lasse of Truth to force him into revealing where the super-humans are being taken.
Batman attracts Superman to the abandoned neighborhood being rebuilt by Wayne Enterprises and fights him with an armored suit, Kryptonite-based weapons and several buildings and vehicles that have been booby-trapped with Batman's arsenal of anti-Superman weapons. The fight is vicious and ends with Superman victorious. Batman urges Superman to kill him, but Superman refuses. Batman then reveals that the fight was designed to test Superman.
When pressed for the signal jammer, Batman declares innocence, and they join forces to locate the true mastermind behind the conspiracy. Simultaneously, Diana locates the Cadmus facility in the outskirts of Metropolis and observers the experiments being conducted therein, particularly on Aquaman, and the ongoing development of the biotechnological weapon, Doomsday.
Wonder Woman infiltrates the facility and rescues Aquaman, but he leaves her behind and returns to the ocean. Luthor's men, armed with advanced weaponry, spring to action, forcing Wonder Woman to flee. Luthor later informs Cale that the Cadmus facility has been compromised, and that they only have no resort to protect their careers.
Batman leads Superman to the Batcave, where they deduce Luthor is behind everything. Diana arrives and reveals that she knows their secret and exposes Luthor's experiments at Cadmus. Superman is infuriated that Luthor has been weaponizing the technology stolen from Zod, as he still blames himself for all the damage it caused.
Superman introduces Lois to Batman and Wonder Woman and they join forces to expose Luthor. Superman, Batman and Wonder Woman attack the Cadmus facility to rescue the remaining prisoners, but are then attacked by Doomsday, who has been deployed by Luthor and Cale. Superman fights Doomsday while Wonder Woman helps the remaining prisoners to flee and Batman retrieves data from the Cadmus' servers and fights Kniazev. Meanwhile, Lois infiltrates LexCorp Tower using the signal jammer while Jimmy creates a distraction to find a way to disable Doomsday.
Doomsday marches to Metropolis, and Cale learns that Luthor has sub-programming in Doomsday to maximime collateral damage to further damage Superman's reputation. Superman, Batman and Wonder Woman battle Doomsday in Metropolis, and are joined by Aquaman, who wants to repay his debt to Wonder Woman and get revenge against Luthor. Together, the heroes manage to minimize collateral damage and avoid innocent casualties, but Doomsday is still able to adapt to their abilities and overpower them in combat.
Mercy catches Lois and they have a fight, but Lois manages to locate Doomsday's systems and insert a sub-routine that allows Alfred to disable the servers. Cale attempts to terminate Doomsday, but Luthor reveals that she can't. When she attempts to expose Luthor, he kills them and makes it appear to be suicide.
Without LexCorp satellites uploading battle tactics directly into his mind, Doomsday becomes more vulnerable to attacks, but continues wreaking havoc and causing wanton destruction. Victor is caught in the crossfire while helping innocents and severely injured. With Batman, Wonder Woman and Aquaman all struggling to protect the innocent, Superman realizes what he must do and soars into Space with Doomsday. He flies into the Sun, with Doomsday still trying to kill him, and they disappear in an explosion.
Superman is believed to have sacrificed himself, but emerges from the Sun and returns to Earth as the planet celebrates his victory.
A few days later, Superman speaks to the Congress once again and speaks in favor of his new allies, as Batman is embraced by the public as reality and the police charges against him called into question, Wonder Woman continues helping people in impoverished countries, Aquaman continues fighting for the environment, Victor is transferred to S.T.A.R. Labs' C.Y.B.O.R.G. Program, Senator Cale is framed of having authorized Doomsday's deployment, and, although Luthor covers up his involvement, his role in creating Doomsday and other Kryptonite-based weapons is exposed and his company loses its military contracts as a result. Superman concludes his statement by revealing that "a new age is dawning."
Luthor is drinking in his office when Superman arrives and they discuss recent events separated by a glass window. Luthor accuses Superman of being the end of human achievements, Superman claims that Luthor takes himself as superior to other humans, and is terrified that for all its wealth and power he is still beneath all the heroes that fought in Metropolis and fight everyday for an ideal grander than themselves. The ideal of justice. Luthor vows to destroy Superman. Superman claims he'll be waiting.
The script concludes with Superman, Batman, Wonder Woman and Aquaman meeting at Kent Farm to discuss Luthor's actions. Superman points out Luthor won't stop, and there'll be others like him. Aquaman claims to have affairs in his "home", but is willing to assist if necessary, as the heroes have earned his respect. After he departs, Superman, Batman and Wonder Woman decide to find others like them of this new emerging race of meta-humans to form a line of defense against Earth and those who seek to bring it harm. Batman points out to reports of a red blur in Central City stopping bank robbers.
Superman asks what happens next. Wonder Woman says "recruitment".
"Dude's corny as fukk, he gave up his powers for an ugly chick, was using his logo as a weapon, my gym teacher is bigger than him and he's smiling all the time"
.... if they pull this off.
