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Three years into his public career as Superman, Clark Kent (David Corenswet) intervenes in a foreign conflict to stop the heavily-armed nation of Boravia from invading its neighbor Jarhanpur. The action is morally clean — Boravia is a clear aggressor, Jarhanpur's civilians are about to be massacred — but politically toxic. Boravia is a US ally, Superman acted without consultation, and within hours the airwaves are filled with congressional voices demanding to know who appointed an alien to redraw foreign policy. The film opens with Superman already losing in the court of public opinion, and never quite lets him recover.

Behind the propaganda campaign is Lex Luthor (Nicholas Hoult), now a tech-billionaire with a contract to operate a black-site detention dimension called the Pocket Universe on behalf of the US government. Luthor has spent years studying Superman's combat patterns through stolen surveillance footage. He has built a private army called the Raptors, funded a tabloid that runs every anti-Superman story on the front page, and bankrolled three superpowered 'meta-humans' — Guy Gardner / Green Lantern (Nathan Fillion), Hawkgirl / Kendra Saunders (Isabela Merced), and Mister Terrific / Michael Holt (Edi Gathegi) — who operate as the Justice Gang, a corporate-sponsored team licensed to fight whoever Luthor's PR cycle has decided is the villain that week.

Lois Lane (Rachel Brosnahan) and Clark have been dating openly for months, a fact known to almost no one at the Daily Planet. Their relationship gets its big stress test in the film's most-quoted scene: a long, single-room conversation in Lois's apartment in which she — half girlfriend, half investigative journalist — sits Clark down for an on-the-record interview about Boravia. Lois argues that Superman cannot keep punching first and explaining never; Clark argues that the cost of asking permission is dead civilians. The scene ends without resolution. Brosnahan plays Lois as the only character in the film who treats Superman like a colleague rather than a god or a threat.

Luthor's first move against Superman is a publicly-staged fight. He releases a brutish kaiju called the Hammer of Boravia into downtown Metropolis to draw Superman out, then arrives in a Lex-piloted exo-suit to 'rescue' the city. Superman is beaten badly, in part because Luthor has been pre-feeding him micro-doses of kryptonite gas through Metropolis's drinking water. Clark crawls home to the Fortress of Solitude, broken-ribbed and dehydrated, and is licked back to consciousness by Krypto, his hyperactive, semi-feral Kryptonian dog. Krypto is comedic relief on the surface and existential weight underneath — the only other Kryptonian on Earth, and a constant reminder that Clark is keeping things alive that he cannot fully control.

At the Fortress, Clark finally plays the full version of his birth-parents' message — a holographic recording from Jor-El and Lara that he has watched dozens of times but never to the end. The complete recording reveals that Jor-El's instructions to baby Kal-El were not the noble 'lead them, inspire them' line Clark grew up with, but a colder mandate to rule Earth — to take as many wives as needed, to seed a new Krypton, to subjugate the inferior species. The message is, in Gunn's words, 'the worst thing Superman has ever read'. Clark, raised by Jonathan and Martha Kent (Pruitt Taylor Vince and Neva Howell) in a Smallville farmhouse on a steady diet of decency, has to confront that his biological parents wanted him to be a conqueror.

Luthor leaks the doctored version of the Jor-El message — translated as 'rule them and grow strong, my son' with the conquest language emphasisizd and the contradictory clauses cut — to the global press. Public opinion turns overnight. Crowds gather outside the Daily Planet calling Superman an alien fifth-columnist. The US government revokes his vigilante immunity. Mister Terrific, Hawkgirl and Green Lantern, who had been suspicious of Luthor's contract but were paid to be his attack dogs, are activated to bring Superman in. The Justice Gang corner Clark in Centennial Park and beat him into a pocket dimension that Luthor has built specifically for him — a black-iron prison floating in a void, custom-engineered with kryptonite walls and red-sun lamps to neutralise his powers.

Inside the Pocket Universe, Clark is held alongside a meta-human named Rex Mason / Metamorpho (Anthony Carrigan), a former scientist whom Luthor cursed with kryptonite-laced shape-changing powers and is now using as a living weapon against Superman. Rex initially attacks Clark on Luthor's orders — his infant son is being held hostage in the same prison — but breaks when Superman refuses to retaliate and instead spends the fight talking him through what Luthor has done to him. Rex agrees to help. Together they spring the other prisoners, and Clark, recovering enough strength to fly, breaches the dimensional barrier and brings everyone home.

By the time Superman returns to Metropolis, Luthor's endgame is already unfolding. Boravia has invaded Jarhanpur a second time, this time openly funded by LuthorCorp arms shipments. Luthor's plan: trigger a regional war that justifies a Justice-Gang-led 'humanitarian intervention,' redraw national borders to grant himself private oil and mining contracts, and discredit Superman as the alien who could have stopped it but chose not to. Clark, Lois, and the surviving prisoners — plus Rex carrying his baby son — race to Jarhanpur, where Superman publicly intervenes to halt the invasion in front of every news camera Lois has tipped off.

The Justice Gang are sent to stop him, but mid-fight Mister Terrific — the team's actual moral conscience — accesses Luthor's encrypted servers and broadcasts the unedited Jor-El message, the doctored translation, and the Pocket Universe footage to every screen in the country. Green Lantern and Hawkgirl turn on Luthor mid-battle. Lex deploys his final weapon, a Superman clone codenamed Ultraman grown from black-site DNA samples, but Krypto bowls Ultraman through three buildings before he can land a punch on Clark. Superman defeats Ultraman with a combination of brute force and pity — the clone has no mind of its own, only Luthor's stolen template — and stops Boravia's invasion live on global TV.

Luthor is arrested by federal agents on live television, charged with operating an unlawful detention facility, illegal weapons sales, and conspiracy. He spits at the cameras that 'You will all thank me one day,' and is led away in handcuffs. Superman gives a brief televised statement: he is not a Kryptonian prince and he is not the conqueror his birth parents wanted him to be. He is Clark Kent of Smallville, Kansas, and from now on he answers to a partner of his own choosing — the press, in the form of Lois Lane and the Daily Planet — for every public intervention he makes.

The film closes on the Daily Planet bullpen. Clark, in glasses and a hopelessly creased suit, sits across from Lois with a half-eaten sandwich, drafting his next column. Krypto sleeps under the desk. Mister Terrific and Rex Mason chat in the lobby; Hawkgirl and Green Lantern have signed on as a new, post-Luthor Justice Gang, this time answering to the public. A mid-credits scene shows the Fortress of Solitude opening to receive a tall, hooded woman speaking Kryptonian — a clear set-up for Supergirl's introduction. Gunn's DCU starts not with a god descending from the sky, but with a journalist who knows his girlfriend is also his editor and is, on balance, fine with it.