Superman kills General Zod when he attempts to kill innocent civilians with his laser vision. After telling the Army that he will help, but only on his terms, he takes a job at the Daily Planet because nobody would question him going to dangerous places.
On the dying planet Krypton, the scientist Jor-El (Russell Crowe) sends his infant son to Earth, along with a genetic codex for the entire Kryptonian race. General Zod (Michael Shannon), who also wants the codex to save the planet, kills Jor-El after the craft is launched. He and his followers are captured and banished to the Phantom Zone, but are freed after Krypton explodes.
On Earth, the spacecraft was found by Jonathan and Martha Kent (Kevin Costner and Diane Lane), who raise the young Kal-El as their own and name him Clark. Since childhood, Clark knew he was different from the others, and Jonathan eventually tells a teenage Clark about the spacecraft. Clark was also told by his father not to reveal his true self, as the world would see him as a threat, not a savior. Now as an adult, Clark (Henry Cavill) is a drifter helping those in need and grieving over the death of his adoptive father.
Clark travels to the Arctic when he hears about a spacecraft found in the ice. Using a control-key that was in his craft, it is able to access a hologram of Jor-El, who tells him everything about who he is and where he came from. Jor-El also gives his son a blue suit with a red cape. Lois Lane (Amy Adams) is a reporter who is also in the Arctic to investigate the craft. She sees Clark go inside it, and she follows, and is promptly attacked by the ship's defenses. Clark is able to save her life then disappears. Lois writes about the man and the craft, claiming both are alien, but her editor-in-chief Perry White (Laurence Fishburne) won't print it.
A UFO shows up, and it's General Zod. He appears on worldwide television and says he is looking for Kal-El. Turn him over and he will spare the planet. Clark sees the message and turns himself in to the Army, wearing the suit and cape. Lois questions him, and starts to call him Superman. Zod's associate Faora arrives and takes Superman and Lois onto the ship, where she must wear a helmet since the atmosphere is not suitable for humans. Superman is weakened by the Kryptonian atmosphere as well.
On the ship, Lois meets the Jor-El hologram, and he tells her how to send Zod back to the Phantom Zone. Zod tells Superman his plan to turn Earth into a new Krypton, which will kill everyone on Earth, but he needs the codex. Superman won't tell him where it is, and he and Lois eventually escape. After they're gone, Zod learns that the codex was injected into Kal-El's bloodstream, and he does not need to be alive to harvest it.
Zod then sends his troops out to get Superman and also to begin terraforming Earth into Krypton with device called a world engine. Lois tells the Army that the ship that brought Superman to Earth is needed to send Zod back, so they go to the farm in Smallville and get it. Meanwhile, Superman is trying to stop the world engine and the Army is attacking Zod's troops. Within a few minutes, Superman destroys the world engine, and his ship is activated, which sends Zod's ship and all of his followers back to the Phantom Zone.
However, Zod wasn't on the ship when it went back and he and Superman begin a huge fight over Metropolis. Since Zod now has the same powers as Superman, neither is able to get the advantage over the other. Their fight leads them inside the train station, where Zod decides to get revenge for his defeat by killing innocent civilians with his laser vision. Superman has no choice but to break his neck, killing him.
Some time later, Superman realizes that he is being tracked by the military. He tells them that he is willing to help, but only on his terms. Afterward, Clark tells his mother that he is leaving Smallville for good and moving to Metropolis. He needs a job that will allow him to travel to dangerous places without anyone questioning him. The movie ends with him taking a job with the Daily Planet.