On the planet Krypton, Jor-El (Russell Crowe) stands by his wife Lara (Ayelet Zurer) as she is going into labor. Soon enough, she gives birth to a healthy baby boy, Kal-El.
Later, Jor-El meets with the Kryptonian Council, telling them that Krypton's core in unstable. They ask if he intends to evacuate the planet, but he says it's too late for that. Before he can divulge his plan, General Zod (Michael Shannon) and his followers break into the council, murdering one elder. Zod asks Jor-El to join him in preserving the superior blood line of Kryptonians, but he refuses. He is taken by Zod's men but promptly escapes them.
Outside, Jor-El sees chaos ensuing around the area. He hops on the back of a winged creature, which takes him to the Genesis Chamber, where little Kryptonian babies are. Jor-El swims to the central hub and retrieves the Codex. He takes it back to the citadel where Lara is with the baby. They are preparing to place him in a ship that will take him to Earth, but Lara feels much sadness with the fact that the baby will never really know them. Jor-El assures her that he will be well. He applies the Codex's to Kal-El's body and leaves him a key with an "S". As they prepare to send him off, Zod and his minions prepare to attack the citadel. Jor-El puts on his armor and fights several Kryptonians off. Zod pleads with Lara to abort the launch, but she sends him out. Zod screams in fury and impales Jor-El. He commands one of his own ships to take Kal-El down, but his ship is shot down, and he and his followers are apprehended.
Zod is taken before the council and is banished into the Phantom Zone, which is essentially a black hole. He vows to Lara that he will find her son. Once he and the other Kryptonians are gone, Lara stands outside as her home is destroyed, but hoping that her son is safe. She is consumed in the planet's destruction as Krypton is obliterated.
Years later, an adult Kal-El, under the name Clark Kent (Henry Cavill), is on a boat with other fishermen going to respond to an oil rig that is on fire. Clark rushes off to save the people trapped in there, and they are amazed to see him walking through fire. The men are rescued, but Clark stays behind to hold back a heavy piece of metal, which falls and takes him into the ocean.
Clark has a flashback to his childhood growing up in Smallville, Kansas. In his elementary school class, a teacher asks him a question, but his heightened senses (x-ray vision, hearing, etc.) are overwhelmed, and he runs and hides in the janitor's closet. His adoptive mother Martha (Diane Lane) comes to school to comfort him. Clark can still hear the other kids talking about him, though.
Several years later, Clark is on a field trip being mocked by a kid named Pete Ross (Jack Foley) while Lana Lang (Jadin Gould) tells him to stop. The bus gets a flat tire and the driver swerves off a bridge and into the lake. The kids almost drown but Clark gets out through the emergency exit and pushes the bus out. He goes back in the lake to rescue Pete. Later, Pete's mother meets with the Kents, thankful for what Clark did, but Clark feels like a freak. His dad Jonathan (Kevin Costner) comforts him and shows him the ship he was found in. He also hands him the key that his real father left him with. Jon acknowledges his son is not from Earth but that doesn't matter to him.
Clark stops at a bar and hears about something spotted nearby in the Arctic. He spots a waitress being harassed by a hick, and he goes to intervene. The waitress says it's not worth it and the hick pours beer on Clark. He walks out, and the hick later finds his truck smashed between two power lines. Clark, meanwhile, hitches a ride.
In the Arctic, reporter Lois Lane (Amy Adams) arrives with a crew, including Clark, to meet with Colonel Hardy (Christopher Meloni) and Dr. Emil Hamilton (Richard Schiff). They are told that they believe there is something resting beneath the ice that came from thousands of years ago. At night, Lois snaps a picture of Clark walking out by himself and follows him. He goes into a cave and follows what appears to be Jor-El's ghost, which leads him to find a large ship. He also spots a device that allows him to place his key in it. Meanwhile, Lois comes in and spots a Kryptonian device and takes a picture of it, provoking it and causing it to attack her. Clark comes back and destroys it. He uses his heat vision to treat Lois's wound.
A rumbling occurs near the base where Hardy and his men are, and they notice the ship rising to the sky and flying off.
In Metropolis, Lois reports a story about her savior, emphasizing his superhuman capabilities, but the story doesn't sit well with her boss and editor-in-chief of the Daily Planet, Perry White (Laurence Fishburne). She takes the story to a guy named Glen Woodburn (Chad Krowchuk) for him to put up on the internet, even though she had originally dismissed his site.
Clark is back in the cave and meets the consciousness of Jor-El, who reveals himself to be his true father. He tells Clark a bit of backstory - the ship he found is a scout ship from Krypton sent to discover other worlds. The planet was flourishing, but the inhabitants squandered their natural resources, leading to the instability of the planet's core. Zod stepped in and tried to stage a coup, but Jor-El sent his son away, and since he was the first naturally born child on Krypton, it was all the more important that he be protected. Jor-El takes Clark to find his suit (the iconic Superman one) and tells him that he will help the people of Earth. Clark goes off testing his flight, soaring across the planet.
Lois continues her investigation of her savior, speaking to the fishermen Clark was with, then to an adult Pete Ross. She is led back to the Kent farm and speaks to Martha. Lois then goes to a cemetery where Jonathan is buried. Clark finds her there and says he does not want to tell his story.
Another flashback shows Clark and Jon getting into an argument while driving. A tornado begins to descend, and everybody runs away. Clark runs back to get his dog out of the truck, but Jon tells him to take his mother and a little girl to safety while he gets the dog. The dog is safe, but Jon's foot is injured by a car that falls on the truck. Clark tries to rescue him, but Jon holds his hand out for him to stop. He allows himself to get taken by the tornado, and Clark screams in sorrow.
Lois's story hits the internet, and Perry is not happy. She says she will retract the story with the excuse that her leads fell through. Perry suspends her for two weeks without pay but says she's doing the right thing for pulling the story back. Meanwhile, Clark goes back home to his mother and tells her he found out where he came from and who his parents are.
At NORAD, General Stanwick (Harry Lennix) is told about a UFO being spotted. The footage hits the news, and is interrupted with a transmission that is broadcast all over the world repeating "You are not alone". The person in the video reveals himself to be General Zod, informing Earth about Kal-El's presence. He issues a warning, saying that if Kal-El does not turn himself in within 24 hours, the people of Earth will suffer.
Woodburn rats Lois out on live television saying she knows where to find Kal-El. Perry warns her but she is arrested by Hardy and the FBI. Back in Smallville, Clark is in a church, hearing the news surrounding him. He has another flashback, remembering when several bullies challenged him to a fight, but they were stopped by Jon. Pete Ross even helped Clark back on his feet. Clark speaks to a deacon regarding his situation, revealing he is the one everyone is looking for. Clark feels that the humans can't be trusted, but the deacon says that he ought to take a leap of faith, and the trust will come.
Clark, dressed as Superman, meets with Stanwick and offers to turn himself in on the condition that Lois is safe. He meets with her in an interrogation room and he tells her the "S" on his chest is a symbol for hope. He also tells Dr. Hamilton, Hardy, and Stanwick that it is clear neither of them trust each other, as they fear he could pose a threat to the safety of other humans.
One of Zod's ships comes down. Stepping out is Faora (Antje Traue), one of Zod's commanders. She has Lois join her and Clark in the ship, giving her a helmet for her to breathe since their atmosphere isn't suited for humans. When they make it to Zod's main ship, Clark becomes weakened, as he had never adapted to a Kryptonian atmosphere. He passes out on the ground.
Clark wakes up in regular clothes outside his family's farm, projected by Zod. He steps in and tells Clark how after Krypton was destroyed, he and his followers were awakened from their imprisonment. They used a ship similar to the one Clark came in to look elsewhere for survivors, but found nobody. They retained armor and other materials and were led to Earth when Clark activated the scout ship in the cave. Zod's plan is to recreate Krypton on Earth, but at the cost of human lives.
Clark is tied down to a table where one of Zod's men tries to extract blood from him. Meanwhile, Lois is met by Jor-El, who helps her navigate through the ship. They are able to adjust the ship's atmosphere to fit humans, which allows her to escape and for Clark to get out as well. As she gets in an escape pod, Jor-El tells her that they can send the Kryptonians back to the Phantom Zone using phantom drives. Faora wrecks the escape pod, causing it to plummet to Earth. With Jor-El's guidance, Clark flies back to Earth and rescues Lois.
Zod goes to the Kent farm and interrogates Martha to find the Codex. He has Faora look in the ship, but she cannot find it. When Zod threatens Martha further, Clark flies in and attacks Zod for trying to threaten his mother. He disables Zod's helmet, which overwhelms his senses as it did to Clark earlier. Faora and another Kryptonian named Nam-Ek come in to attack, but the military fights back. A battle ensues, with Faora taunting Clark with her advanced strength and capabilities. Nam-Ek takes down a chopper with Hardy in it, but Clark saves one soldier, as well as Hardy, who is almost killed by Faora. She is taken out by a missile, but is not killed, and is taken back into the ship. Hardy acknowledges that Clark is not an enemy, and Clark thanks him for that.
Zod learns that the Codex lies within Clark's DNA, and that he does not need him alive to extract it from him. He orders the World Engine to be released. This causes one part of his ship to fly down to the Indian Ocean, while the main part descends upon Metropolis. Dr. Hamilton determines that Zod is attempting to recreate the Kryptonian atmosphere and trying to kill off the humans. He and Stanwick are informed of Superman's arrival (as they now refer to him). He and Lois plan on using his old ship to collide with Zod's, as it is powered by a phantom drive, which they realize would open a black hole. Superman flies off to the Indian Ocean while Lois, Hamilton, and Hardy take the ship to Metropolis.
Zod goes to the Genesis Chamber to repopulate the planet with other Kryptonians. After arguing with Jor-El's ghost, he carries on with the plan. Meanwhile, Superman makes it to the World Engine, which attacks him as he is vulnerable to it. At the same time, Zod's ship is destroying Metropolis. Perry and two other Daily Planet members run from the chaos.
Lois tries to activate the ship with the key, but it won't go in. Faora and the other villains attempt to attack, but Hamilton notices the key won't go in because it is exposed to the sunlight. He has it go in, activating the ship. At the same time, Zod comes in with the Genesis Chamber, but Superman flies in to stop him. Zod tells him if he destroys the ship, he destroys Krypton. Superman hesitates but he brings the ship down with his heat vision.
Faora attempts to kill Hardy again, but he echoes a statement she made earlier - "A good death is it's own reward". As the ship is activated, Lois is pushed out of the jet while Hardy flies the jet into Zod's main ship, causing the Phantom Zone to be open and sending Faora and company back there once and for all.
Superman comes down and kisses Lois. They see that Zod is still alive, and he attacks Superman after stating that everything he had done was for the greater good of Krypton. They engage in a battle that causes much more destruction to Metropolis, leading them to crash into a building. Zod attempts to fry a family of four with his heat vision, but Superman pleads with him to stop. When Zod refuses, he sees no other way out, and he brutally snaps Zod's neck, killing him. Superman cries out in regret as Lois comes in to comfort him.
In the desert, Stanwick sees one of his drones come crashing down. Superman knows that he is trying to locate his home, and that he will know if he is looking for him. Stanwick wants to know how he can be sure if Superman will ever become a threat to the country, but he assures him, "I'm from Kansas. I'm as American as can be." He also says he will trust Stanwick.
Clark goes back to Martha, and they both know that Jon would have been proud to see the man he became. Martha asks what Clark will do now, and he says he's gotten a job where nobody would question him for going to strange places - the Daily Planet. Under the identity of Clark Kent, he goes to work and is formerly introduced to Lois, who recognizes him even with his glasses. She welcomes him to the Daily Planet, and he says he's happy to be there.
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