On the planet Krypton, Jor-El helps his wife, Lara, give birth to their child, a son they name "Kal-El." Jor-El then meets with Krypton's Council and argues that the planet's core is collapsing, having been rendered unstable due to the Council depleting natural resources against his warnings; they only have a short time until Krypton explodes. As he pleads with the Council to give him access to the Genetic Codex, the session is interrupted by General Zod and his soldiers staging a coup. Zod tries to persuade Jor-El, his close friend, to join him in his rebellion against Krypton's Council, but Jor-El refuses and is taken away. With the help of his AI assistant Kelex, Jor-El subdues his captors and contacts Lara to tell her to prepare Kal-El's ship for departure.
As all-out war engulfs Krypton, Jor-El hops on his mount, H'Raka, and flies to the Central Hub, where he retrieves the Codex, the repository from which all Kryptonians are genetically engineered for pre-determined roles in society. He escapes from Zod's men when they corner him and makes it back home to his citadel, where he and Lara make final preparations to save their newborn son from Krypton's imminent destruction by sending him to Earth, a distant world orbiting a yellow star; Jor-El assures his hesitant wife that exposure to the radiation of Earth's sun will give Kal-El exceptional abilities. After fusing the Codex into Kal-El's cells and placing the child inside his spacecraft, Jor-El fashions a command key which he then places into his son's capsule.
As Zod and his forces advance on the citadel, Jor-El dons battle armor while Lara makes final preparations for Kal-El's launch. After Zod enters the citadel and demands that Jor-El hand over the Codex, Jor-El stands firm and informs Zod that he and Lara conceived a son naturally, meaning Kal-El will be able to follow his own path in life. Enraged by this, Zod engages his former friend in a violent fight, but Jor-El beats him down. Zod then pleads with Lara to not launch Kal-El's ship, but Lara ignores him and the ship takes off. In a fit of anger, Zod mortally wounds Jor-El with a blade hidden in his gauntlet, then exits the citadel and orders for Kal-El's ship to be shot down, only for the Sapphire Guard to arrive and place Zod and his followers under arrest. Zod and his men are charged with high treason and sentenced to the Phantom Zone. Zod rants at the Council and angrily vows to Lara, who's present at the trial proceedings, that he will find her son and the Codex. Zod and his men are then put into stasis and brought aboard the Black Zero, a gigantic Kryptonian ship that is then placed into the Phantom Zone. Afterwards, Lara watches as Krypton begins to explode; her final words are a prayer that her son creates a better world than Krypton's. Krypton explodes, killing all its inhabitants. Light-years across the galaxy, Kal-El's ship makes its way to Earth, where it crash-lands in a field in Smallville, Kansas.
33 years later, Clark Kent is working on the Debbie Sue, a fishing boat which receives a distress call from an oil rig. Clark disappears from the boat and goes to the rig, where he rescues the crew who witness him use Super Strength to keep the rig from falling long enough for them to escape. An exhausted Clark falls into the ocean. A flashback to Clark's childhood shows that his superhuman powers began to emerge when he was a child attending elementary school. Overwhelmed by his Super Senses, he flees the classroom and locks himself in a closet. His adoptive mother, Martha, is called to the school and she helps Clark get a handle on his abilities. Back in the present, Clark wakes up and makes his way to shore, where he steals some clothes for himself before continuing on. Seeing a school bus pass by causes Clark to remember how, at the age of 13, he used his Super Strength to rescue his classmates after their bus crashed into a river. Pete Ross's mother tells the Kents about Clark's astonishing feat, but the elder Kents deny that there's anything special about their son. Clark's adoptive father, Jonathan, finds Clark sitting alone outside and chides him for risking exposure, telling him that people are afraid of what they don't understand. When Clark presses him for answers , Jonathan shows him the spaceship he arrived in years ago, revealing that Clark is an alien. He gives Clark the command key and tells his son that, somewhere, he has another father who gave him another name, and that Clark was sent to Earth for a reason.
Sometime later, Clark lands a job at a roadside bar, where he overhears two military officers discussing a mysterious object found under the ice in the Arctic. A rude trucker, Ludlow, makes unwelcome advances towards a waitress, prompting Clark to step in. Ludlow publicly humiliates Clark, who then storms out of the bar. Ludlow later finds his truck wrecked with logs. Far off, Clark continues on his way.
Daily Planet reporter Lois Lane arrives at the Arctic, where the US military has set up an installation led by Colonel Nathan Hardy and including Dr. Emil Hamilton from DARPA. Imaging has turned up a massive object that's nearly 20,000 years old. Later that night, Lois follows Clark as he ventures out alone to find the unidentified object, which turns out to be a large alien spacecraft. Aboard the ship, Clark is accosted by a robot sentry until he inserts the command key, activating the ship's systems. He's then forced to come to Lois's aid when the sentry seriously wounds her; after neutralizing the sentry, he uses heat vision to cauterize her wound and leaves Lois outside to be found. The ship then takes off as everyone else watches. Lois writes an article about what she saw in the Arctic, but her editor, Perry White, refuses to publish it, so she has Glenn Woodburn "leak" the story on the Internet.
After the ship settles down on Ellesmere Island, Clark is met by an interactive holographic projection of Jor-El who reveals to Clark his lineage, then exposits about Krypton's history and society: Kryptonians, during an era of expansion long ago, launched thousands of scout-ships into space until the establishment of population control and genetic engineering ultimately led to Krypton's ruin. Jor-El also divulges he and Lara conceived Kal-El in rebellion against Krypton's system of societal conditioning. Clark notes he's alone in the universe, but Jor-El encourages him to be an example to humanity to achieve greatness, presenting his son with a blue suit bearing a red cape and the House of El coat of arms which means "hope." Donning the suit, Clark exits the scout-ship and, remembering Jor-El's words telling him of how Earth's sun empowers him, masters the power of flight.
Lois tracks Clark to Smallville, where she meets him at his adoptive father's grave. Clark dissuades her to not publish her article about him because people aren't ready to accept him. A flashback shows Clark, in his late teens, having a heated discussion with Jonathan about leaving the farm; in a fit of frustration, Clark rejects Jonathan and Martha as just the people who found him in a field. Jonathan concedes his son's point, but before he can elaborate, a tornado makes its way through the area. Clark and Jonathan help people evacuate their vehicles, but Jonathan ends up trapped in the Kents' truck. He gets out, but is too late; Clark prepares to save his father, but Jonathan silently dissuades him from doing so in order to preserve his secret. The farmer is then swept away by the tornado, much to Clark's grief. Lois, moved by Clark's story, decides to kill the article, but is put on three-week leave by Perry, who believes her story but anticipates that people will react negatively to a super-powered alien on Earth. Clark, meanwhile, returns to the Kent Farm and happily reunites with Martha, sharing what he found out about his origins.
The Black Zero appears in Earth's system, and Zod broadcasts a threatening message to the planet, demanding that Kal-El be turned over to his custody or war will follow. Woodburn reveals that Lois knows Kal-El, leading to Lois being cornered by the FBI and Hardy as she attempts to flee Metropolis. In Smallville, Clark seeks guidance from local priest Father Leone, who advises him to take a leap of faith; Clark also recalls another childhood incident in which he was bullied and Jonathan told him that he would grow up to change the world and that it's up to him to decide what kind of man he wants to become. Clark, wearing his Kryptonian garb, turns himself over to the military, led by General Calvin Swanwick, on the condition that Lois is freed. The military is ordered to hand Clark over to Zod, to which Clark offers no resistance. A Kryptonian ship arrives, and Faora, Zod's second-in-command, demands that Lois accompany her and Kal-El. Lois obliges, and they are brought aboard the Black Zero, where they are brought before Zod, who civilly greets Kal-El. Clark collapses onto the floor; Zod explains that Clark's physiology, having lived on Earth all his life, isn't suited to a Kryptonian environment.
Clark passes out and wakes up in a mental simulation where Zod explains how he and his followers were freed from the Phantom Zone after Krypton's destruction and they spent the past 33 years searching for any Kryptonian survivors, salvaging weapons and equipment from long-dead Kryptonian outposts, including a World Engine. Zod reveals that Clark activating the scout-ship's distress signal drew Zod and his men to Earth, then shares his plan of terraforming Earth into a new Krypton so he can repopulate the planet with new Kryptonians engineered from the Codex that Jor-El sent with Kal-El. Clark refuses to have anything to do with Zod's genocidal plans and comes out of the simulation, still weakened and bound to a lab table. Zod reveals he killed Jor-El years ago and leaves the room. Jax-Ur, a scientist, extracts a blood sample from Clark.
Lois, thrown into a cell after being interrogated by Zod, uses the command key to install Jor-El's Digital Avatar into the Black Zero's systems. Jor-El changes the ship's environment to Earth conditions, restoring Clark's powers, and helps Lois make her way to an escape pod, telling her how to send Zod and his men back to the Phantom Zone. Lois flees the ship inside the pod, which is damaged by Car-Vex, one of Zod's soldiers. Jor-El then appears before Clark to impart final words of wisdom, encouraging him to save Lois and all of humanity. Clark then flies to Earth, where he saves Lois from the burning escape pod.
Zod, Faora, and a couple of their fellow soldiers go to the Kent Farm, where they interrogate Martha about the Codex's whereabouts. Clark arrives and tackles Zod, punching him in a rage as they fly across Smallville before crash-landing in the town center. Zod's helmet is damaged and his senses are overwhelmed as he is exposed to Earth's atmosphere. Clark taunts the weakened general and is blasted by an arriving Kryptonian vessel. Zod is escorted away while Faora and Nam-Ek remain behind to battle Kal-El in a destructive confrontation throughout Smallville. The US military, led by Hardy, also arrive and engage all three Kryptonians; Faora easily dispatches many of the human soldiers while Clark eventually sends Nam-Ek crashing into a nearby train yard. Clark then tackles Faora just as she's about to fight Hardy one-on-one, only to be hit by a train thrown by Nam-Ek and sent crashing into the nearby Sears. A missile hits Faora, knocking her out, and Nam-Ek departs with her. Clark emerges from the ruins of Sears before Hardy and his soldiers; Hardy respectfully declares that Clark is not the enemy. Clark thanks the colonel for his show of respect and flies off to the Kent Farm to check on Martha. Lois arrives with news of how to defeat Zod and his men.
Back aboard the Black Zero, Zod learns from Jax-Ur that Jor-El infused the Codex into Kal-El's cells; after Jax-Ur confirms that Kal-El does not need to be alive in order for the Codex to be extracted, Zod orders for the World Engine to be deployed. The World Engine detaches from the Black Zero and lands in the Indian Ocean while the Black Zero itself repositions itself over Metropolis. As the World Engine begins its terraforming process, Dr. Hamilton notes what exactly is going and warns that, once its finished, there won't be a human race left. Clark (now called "Superman"), Lois, and Hardy arrive with Kal-El's ship in tow, explaining to Swanwick and Hamilton that both the Black Zero and Kal-El's spacecraft are powered by a Phantom drive and that causing the two to collide will create a singularity that will suck Zod and his soldiers back into the Phantom Zone. Swanwick assents to the plan, and Superman flies off to destroy the World Engine.
Kal-El's ship is loaded aboard a military plane that heads to Metropolis, where the Black Zero, working in tandem with the World Engine, is causing massive destruction in the city. Zod heads to Ellesmere Island, where he hones his heightened senses before entering the scout ship and installing his own command key, giving himself control of the craft. Jor-El appears and tries to talk Zod out of going through with his plan to re-build Krypton by destroying Earth and humanity, but Zod cruelly rebuffs his former friend and deletes his program from the ship's systems before taking the controls and flying to Metropolis. Superman battles the World Engine's defensive measures despite the toxic atmosphere its generating, then gathers his strength and flies straight into the World Engine, destroying it.
As the military plane flies toward the Black Zero, Lois tries to insert the command key into Kal-El's ship, but it won't go all the way in. Zod arrives aboard the scout ship, taking down other military planes, and prepares to fire on the main plane until Superman arrives and crashes into the scout ship. Ignoring Zod's claim that destroying the scout ship will eliminate any chance of re-building Krypton, Superman declares that Krypton had its chance and uses heat vision to destroy the Genesis Chamber aboard and damage the scout ship itself, causing it to crash-land in the middle of Metropolis. Faora heads off the Black Zero and boards the military plane, taking out a number of military personnel before coming face-to-face with Hardy once again just as Hamilton succeeds in inserting the command key. Hardy takes the controls and flies the plane straight into the Black Zero, causing a massive energy surge that sends Lois falling out of the plane. The resulting singularity sucks in Faora, Hardy, Hamilton, and the Black Zero crew. Superman emerges from wreckage and flies up into the air to rescue a falling Lois, straining against being pulled into the Phantom Zone himself. The singularity ends, and Superman and Lois touch down on the ground and share a passionate kiss.
Zod emerges from the wreckage of the downed scout ship, and Superman flies over to him. A defeated Zod vents his anger and grief over losing the chance to re-build his long-dead homeworld and no longer having any purpose in life. He then attacks Superman in a rage and vows to kill every last human on the planet, prompting a colossal battle throughout much of Metropolis. At the height of their fight, Zod sheds his battle armor and masters the power of flight. After flying through the city, exchanging more blows, and wreaking untold destruction, Superman and Zod crash-land in a train station, where Zod turns his heat vision on a nearby innocent family. Superman pleads with him to stop, but when Zod perists, he is forced to snap the general's neck, killing him. A horrified Superman cries out in sorrow, and Lois arrives to comfort him.
Sometime later, Superman throws a surveillance drone in the path of Swanwick's oncoming car before touching to talk with the general. He assures Swanwick that he's here to help and convinces him to allow him to act independently, to which Swanwick grudgingly agrees. In Smallville, Clark meets with Martha as they visit Jonathan's grave and wishes his adoptive father could've seen what he's become, and Martha replies that Jonathan sensed Clark's potential years earlier. Martha then asks what Clark's going to do when he's not saving the world, and Clark tells her he has to get a job where he can keep his head to the ground and no one will get suspicious when he wants to go to dangerous places.
At the Daily Planet, Clark Kent, wearing a pair of glasses to disguise himself, is introduced as a new reporter to Steve Lombard and Lois, who tells him, "Welcome to the Planet." Clark replies, "It's good to be here, Lois," and shares a smile with her.