On the planet Krypton, Lara Lor-Van has just given birth to Kal-El with the help of her husband Jor-El. Jor-El travels to Kandor on his pet H'Raka where he stands in front of the Kryptonian Law Council telling them the planet is to explode because of the council's decision to harvest the planet's core to serve the depleted energy reserves of the planet. They dismiss his claims but General Zod takes note informs Jor-El he is going to overthrow the council. A concerned Jor-El steals the Growth Codex (the source of the artificially-produced masses of genetically-specialized citizens of Krypton) and graphs the atomized particles onto Kal-El's red blood cells. Kal-El is revealed as the first naturally-born kryptonian in centuries. His parents then put the Command Key and their son into a ship. Zod discovers their plan and attacks Jor-El. Jor-El battles Zod who kills Jor-El while Lara launches Kal-El's ship to Earth. The Sapphire Guards save Kal-El's ship from being shot down and arrest Zod. Zod and his followers are imprisoned and sent to the Phantom Zone before the planet Krypton explodes. Kal-El lands in the field of Jonathan and Martha Kent.
Kal-El, now known as Clark Kent and an adult, is now working on a crab boat when an Oil Rig in the distance is on fire. Jumping overboard and swimming over, he begins to help people get to safety as the Coast Guard arrive to get people to safety. When a piece of rigging threatens to fall on them, Clark holds it up long enough for them to get clear before an explosion sends Clark flying into the water. While unconscious, Clark remembers back to being 9 when his Super Hearing and X-Ray Vision first manifested at school and Martha helped him control his powers.
Returning ashore, Clark steals some clothes and skips town, seeing a school bus on the way reminding him of when he was 13 and was bullied by boys in his class. The school bus they were on crashed over a bridge and Clark saved it from drowning. Revealing his powers to Lana Lang and Pete Ross. Back home Jonathan revealed to Clark the reason for his powers by showing Clark his ship in the barn and giving him the Command Key.
Clark is now working in a highway bar where he overhears some men talking about the military looking for an alien ship under the ice of Ellesmere Island. An argument breaks out soon after, and Clark destroys the truck belonging to the man responsible before skipping town in the direction of the alien ship.
Lois Lane arrives via chopper to cover the alien ship and has her bags carried by Clark who is now working there. The operation led by Colonel Hardy who is working with Emil Hamilton. Emil is not pleased to see Lois there and tries to get her away. Clark, away from the military, burrows through the ice with his heat vision before being attacked by the ship's defenses. Lois sees this and follows him, but is also attacked by the defenses. Clark saves her and reveals his powers to her. He takes her outside before returning and activating a projection of his real father Jor-El, who informs Clark of his name and purpose on Earth. The ship then launches from the ice and rests on a nearby mountaintop before Jor-El reveals the history of Krypton before Clark finds a suit, which he puts on and goes outside learning to fly before zooming off into the sky.
General Zod and his minions, in space searching for Kryptonian survivors and retrieve an ancient Terraforming Generator before they pick up the ship's signal and track it to Earth.
Lois returns to Metropolis to tell her editor Perry White she is dropping her story on the alien ship and is given 2 weeks leave. She uses it to begin investigating Clark's life and his history of saves over the years, including talking with a grown Pete Ross before turning up at the Kent Farm where Clark recently returned home. Lois visits his father's grave where he arrives and tells her the story of how he died helping people during a tornado and died keeping Clark's abilities a secret.
Zod arrives in Earth's orbit and transmits a message across the world to every electronic device requesting Kal-El to be handed over. Clark sees this and visits the priest at the church who advises him on what he must do. Clark decides that he can't put humanity at risk.
He flies to Edwards Air Force Base where he surrenders himself. Lois talks her way into getting access to him before Kal tells them he is not their enemy. He soon meets on the desert with Zod's ship where he is greeted by Faora Hu-Ul who requests that Lois come too, whom Kal slips the Command Key. Lois is given a visor to help her breathe and the atmosphere aboard Black Zero interrupts Kal's powers. He is strapped down and meets General Zod who wants Kal to join him to rebuild Krypton on Earth. Zod has the Jax-Ur project images into their minds and probes their thoughts before he takes his forces in search of the Codex. The Jor-El AI which Lois activates helps her escape into a pod which jettisons to earth. Kal escape