The story opens on the Planet Krypton, wherein Lara Lor-Van (Ayelet Zurer), has just given birth to a son. She and her husband Jor-El (Russell Crowe) have birthed their son naturally and in violation of the basic laws of the planet, where babies are to be bred through genetic engineering with a planetary 'Codex' that imprints what a person's place in life is to be (leader, scientist, general, etc).
Jor-El and his wife have chosen this path as their planet is on the brink of destruction. Harvesting their planet's core for resources has made it unstable and it will destroy itself. After the birth of his son, Jor-El appears before the Kryptonian Leaders, pleading with them to allow him to save the planet's Codex, and to search for a habitable world beyond Krypton.
However, even with destruction imminent, the council will not abandon its ways. The council is set upon by General Zod (Michael Shannon) and numerous followers, intending to take control of the planet. Though Jor-El does disagree with Council, he refuses to join Zod's coup. Zod orders Jor-El to be arrested, but Jor-El escapes and flees to an area nearby, wherein the planet's birthing chamber resides.
Right before he leaves, he tells Lara to prepare the small spacecraft he has built to transport his son from Krypton and to find a suitable world to send him to. Stealing the Codex from the chamber, Jor-El races back to his home where his wife Lara has found a planet to send their baby to: Earth.
Though Lara is sad at the loss of their child, Jor-El claims he will live his life in a new way: free of the limitations imposed by Kryptonian society. Their son, Kal-El, will be able to choose his way in life. Lara worries about their son's ability to survive on his new planet; Jor-El assures her he will be stronger, faster, invulnerable and possess powers that will make him a super-being there because of Earth's yellow sun.
Jor-El places the Codex into a device that bonds it to his son's living cells. As they prepare to launch the pod containing their son, Zod and his followers force their way into the Els residence, demanding that Jor-El hand over the Codex. Jor-El claims it is in the pod with his son. Zod becomes enraged and attacks Jor-El, eventually stabbing him to death.
During the fight, Lara engages the pod's engines and it shoots into the sky. Angered that Jor-El and his wife have doomed the Kryptonian race with the removal of the Codex, Zod orders his followers to shoot down the pod. However, his orders are suddenly cancelled when Kryptonian security ships appear, destroying the attacking vessel and arresting Zod and his minions.
In the confusion, a Phantom Drive engages on the pod, rocketing the baby away in the blink of an eye. Zod and his followers are banished to The Phantom Zone. In a fury, Zod lashes out, declaring the leaders will not grant him and his followers a quick death. He also swears to Lara (who is present), that he will find her son.
Zod and his followers are placed in a giant craft, the Black Zero, that is sent into the Phantom Zone. Shortly after, Krypton's core collapses as Lara watches the planet breaking apart. Many worlds away, the pod carrying Kal-El rockets into Earth's atmosphere, touching down somewhere in the Great Plains of the United States.
The scene then shifts to ocean waters, where we see a bearded man (Henry Cavill) working aboard a fishing vessel and having trouble concentrating on his duties.The crew are soon alerted to a distress call for help from a flaming oil rig. The bearded man quickly disappears from the ship but is on the rig moments later, rescuing the crew and getting them to board a Coast Guard chopper.
He is unable to join them, as he rushes to keep a part of the rig from collapsing on the landing pad. As the chopper flies away with the rig's crew, the rig collapses down on him and he ends up floating in the water. We soon learn that this is Clark Kent, as in a deep mental state, he recalls when he was younger, and manifested X-Ray vision, and super-hearing.
Scared at what he was seeing and hearing, Clark runs from his classroom and locks himself in a closet. His Mother Martha Kent comes to the school, and manages to coax him out, helping him to focus his powers, quelling the myriad sounds he hears.
Back in the present-day, Clark has managed to return to land and steals some clothes. As he attempts to figure out where he is, he sees a school bus nearby. Clark has another flashback to when he was 13. He recalls being picked on by a boy named Pete Ross (Jack Foley), before the school bus they were on suddenly blows a tire, and careens off a bridge into a river.
Thinking quickly, Clark escapes out the rear emergency door, and pushes the bus to shore. Clark jumps back into the water and pulls the very boy who harassed him to safety. Though Pete's mother claims that Clark miraculously saved the occupants of the bus, Clark's father Jonathan Kent (Kevin Costner) tries to convince her otherwise.