The film starts 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, in violation of the basic laws of the planet, where babies are to be bred through genetic engineering with a planetary 'Codex' that imprints just 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 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 agree the Council's ways are not right, 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.
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. 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 Kryptonians. Their son,
Kal-El, will be able to choose his way in life.
As they prepare to launch the pod containing their son, Zod and his followers enter their residence, demanding that Jor-El hand over the Codex. Jor-El claims it is in the pod with his son, causing Zod to battle Jor-El, before stabbing him to death. In 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, arresting them. In the confusion, a Phantom Drive engages on the pod, rocketing the baby away in the blink of an eye.
For punishment, Zod and his followers are banished to The Phantom Zone, causing Zod to lash out that even though their planet will soon be gone, 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.
Shortly after, Krypton is destroyed. Many worlds away, the pod carrying Kal-El rockets into Earth's atmosphere, touching down near Smallville, Kansas.
The scene then shifts to ocean waters, where we see a bearded man (
Henry Cavill), having trouble watching what he's doing. However, 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. 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 borrows 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 emergency door, and pushes the bus to shore, along with saving Pete.
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. Needless to say, Clark feels even more conflicted, as his father has tried to tell him to suppress his powers, but Clark was torn by a need to help others.
When Clark demands to know what's wrong with him, Jonathan shows his son the pod he came to Earth in, along with a strange metallic item that was found with him. Jonathan claims he had a metallurgist examine it, but it is comprised of elements not found on Earth. Imprinted on the small fragment of metal is a shield-like shape containing an "S".
The scene then returns to the present day, where Clark has gotten a job at a truck stop in Canada. As he works, he hears some military men talking quietly about some object found in the ice a ways north of the stop. When a trucker comes in and starts harassing one of the waitresses, Clark attempts to stop him, but afraid others will see his powers, stands there and takes the trucker's taunts. Without saying a word, Clark takes off his apron and leaves the stop. Later, as the trucker leaves, he is shocked to find his rig impaled on several of the tree logs he was hauling.
The scene then cuts to Lois Lane (Amy Adams), landing at the base in Canada, where she is met by Professor Emil Hamilton (Richard Schiff), and Colonel Nathan Hardy (Christopher Meloni). Drilling is still commencing within the ice to get to the craft, but ice drilling tests have at least confirmed that the ice surrounding the object is thousands of years old.
Going out in the evening to shoot some pictures, Lois is shocked when she checks them, to see a man walking on a ridge near the drilling site, not wearing any cold-weather clothing. She sneaks up to where he was, and finds a tunnel bored into the ice.
This is Clark's doing, as he had followed the word of the Military men, and made his way to the site, using his heat vision to tunnel into the ice. He then finds a strange spacecraft, and going inside, finds a panel that opens up. It contains a hole, that seems to match the shape of the object his father found with him in the pod. Entering it into the hole causes a person to suddenly appear nearby. He doesn't say a word, but just starts walking off. Clark attempts to catch up to this person, but he always seems to be several steps ahead of him.
Meanwhile, Lois has found her way onto the ship, but is attacked by a sentry. Her screams cause Clark to come running. After dismantling the sentry by crushing it with his bare hands, he sees that Lois has a wound in her lower abdomen. He tells her she's bleeding internally and uses his heat vision to cauterize the wound.
Shortly after, military forces nearby are all surprised when the ice starts to crack, and a giant ship emerges, flying off.
Lois is found the next day, and shortly thereafter, writes up an article about what she experienced. However, her editor at the Daily Planet, Perry White (Laurence Fishburne), refuses to publish it. Even the Pentagon has denied her 'aliens and spaceships' story. Lois then attempts to play hard ball. Going to a contact of hers named Glen Woodburn (Chad Krowchuk), she allows him to publish her story. Though he cautions that she could get in trouble for leaking the story, she claims she wants to do this, in hopes that it will catch the attention of the person she met.
Meanwhile, Clark has piloted the spaceship to another remote location in the Arctic. It turns out the figure he was following is a hologram of his Father Jor-El, who is appearing via the 'key' Clark inserted into the ship. Jor-El explains the history of the planet Krypton and that the ship Clark found was a sentry ship sent out many years before, when the the council of Krypton had attempted to colonize other planets.
Also on board the ship, Clark finds a suit that he puts on, and finds out that the crest on the suit (and on the key he had), is a symbol of hope and the symbol of his true family. Jor-El also explains that the planet's sun has made Clark stronger, and has been helping him manifest powers for some time. Hearing this, Clark begins to push his powers: first taking flying leaps, before eventually being able to fly.
Back in Metropolis, Perry White is furious that Lois leaked her story to the internet, and suspends her for three weeks. Lois uses this time to begin tracking down leads to her mystery man. Her sleuthing leads her to Smallville, and eventually, Martha Kent
Visiting the grave of Jonathan Kent, she is surprised when her mystery man appears (albeit in nondescript clothing). Lois claims she wants to tell Clark's story, but he tells her of how he abides by his father's request to not reveal himself until the world 'was ready.'
Clark then relates how Jonathan died. After the two have an argument during a drive, they stop the vehicle they are in when a tornado forms. Clark gets his Mom and several others to safety, with Jonathan attempting to get the family dog free of their vehicle. The dog makes it to safety, but Jonathan ends up injuring himself, unable to make it to the overpass where everyone has taken shelter. Clark attempted to help his father, but a gesture from Jonathan cautioned him to not reveal himself, leaving Jonathan to be swept away by the tornado. Hearing this story, Lois respects Clark's wish for privacy, and stops trying to pursue a story from him.
Clark returns to his Mother, and happily tells her that he has found where he came from, and who his true parents are. Though Martha fears that her son will now be taken from her, Clark assures her this won't happen.
Meanwhile, the military has received word of a strange ship in geosynchronous orbit around the planet. Soon, others report the strange sighting, but are surprised when power is cut off to all parts of the world, and a message is broadcast...from General Zod. Zod demands that the people of Earth hand over Kal-El within 24 hours, or there will be consequences. A worldwide manhunt is initiated to find this Kal-El. Glenn Woodburn is interviewed about the aliens, and drops Lois' name, which soon results in numerous FBI agents being sent to intercept her. She is then held in custody by the army.
Back in Smallville, Clark goes to a local church, and confesses to the pastor there, that he is the one the aliens want. Though he admits he is conflicted: he doesn't trust that Zod will leave Earth in peace, but he is also wondering if he should trust humanity. His decision is made when the Pastor tells him that sometimes one must take a leap of faith.
Clark then appears before the Army in his Kryptonian suit, willing to surrender on condition that he can meet with Lois, and that she be freed. Clark is handcuffed (mainly as a way for the military to trust him), and he and Lois have a short conversation, before he is to be handed over to Zod.
A black craft appears to bring him to Zod's ship. The craft is commanded by Faora-Ul (Antje Traue), who also demands of General Swanwick (Harry Lennix), that Lois also be taken with them. Though Swanwick points out that the deal was originally for Kal-El to be handed over, Lois goes along. Before they reach Zod's ship, Lois is fitted with a breathing apparatus, as the atmosphere on the ship will not be suitable for her. When Faora's attention is turned, Clark slips Lois the key he used to restart the Arctic ship.
On board the ship, Zod welcomes Clark, who few moments later, collapses to the floor of the ship. Though Lois is worried for him, Zod assures her that Clark's body is simply adjusting to the Kryptonian atmosphere aboard the ship.
Clark passes out, and finds himself in a dreamlike vision of his family's farm. Zod explains to Clark that after the destruction of Krypton, the portal to the Phantom Zone where they were trapped, was opened again. Utilizing the portal's Phantom Drive, they were able to transport themselves all across the galaxy. Searching out the various planets which colonizing ships were sent, their searches for a new planet proved unfruitful, as each of the colonists sent to these various planets were found to have perished. However, Zod and his followers took what they could from the remnants of their civilization, including a "World-Building" machine.
When Clark activated the ship in the Arctic, it sent out a signal, which lead Jor-El to Earth. Jor-El claims that he then intends to turn Earth into a New Krypton, but Clark is unwilling to go along with this plan.
Awakening from the vision, Zod tells Clark that with or without him, he will revive their civilization. As well, Clark's adjustments to the ship, have made him as strong as the other Kryptonians on it. This allows one of Zod's men, Jax-Ur (Mackenzie Gray), to obtain a blood sample from Clark.
Meanwhile, Lois is thrown into a holding cell, where she comes across a panel with a small hole. Lois notes it is the same size as the key she has. Inserting it allows the information from Jor-El to appear before her. The key causes the ship's atmosphere to alter towards more suitable conditions for Clark and Lois, and Jor-El gives Lois valuable information for stopping Zod, along with leading her to an escape pod.
The changing of atmosphere allows Clark to break his bonds, and Jor-El appears before him, pointing out that Lois needs to be saved (as her escape pod was ruptured by laser fire).
Clark manages to save Lois from the pod, but his attention is soon drawn to his Mother, who is set upon by Zod and Faora, come to the Kent farm, looking for the Codex. Faora finds Clark's pod, but no sign of the Codex. When Zod threatens Martha, Clark races to save her, hitting Zod with such force, that the two end up thrown into the heart of downtown Smallville.
Upon recovering, Zod's face-mask short-circuits, and his body begins to adapt to the Earthen environment, as he suddenly gains X-Ray vision, and his hearing begins to take in everything at once (just like Clark did when he gained these powers long ago). The overload to his senses forces Zod to temporarily retreat.
Clark claims that his parents helped him hone his skills to control the sensory overload, but his assurance is thrown aside when a ship recovers the stunned Zod, and Faora and a larger Kryptonian (Nam-Ek) attempt to bring Clark down.
Word of the alien presence in Smallville has reached the Army, and Col. Hardy approaches with helicopters and planes. Hardy claims that all three of the aliens (including Clark) are hostile, and all form of weaponry are thrown at them.
Though Faora and Nam-Ek escape, Clark is able to change Hardy's mind when he saves the Colonel along with several other soldiers.
Clark returns to his Mother, but also encounters Lois, who explains to him what Jor-El told her on the ship.
Back on his ship, Zod is informed just what happened to the Codex. It seems that Jor-El had it transplanted into Clark's cells, making him the source to create new Kryptonian life. When Zod is informed that Clark does not need to be taken alive to redeem the Codex, he puts his plans into effect.
Zod then launches the World-Builder. As it touches down near the South Indian Ocean, Zod's ship hovers over Metropolis. Using the Phantom Drive, Zod switches on the World-Builder, which creates a link with the ship through the Earth, beginning the process of terraforming Earth, creating a stronger gravitational pull. This causes cars to flatten in Metropolis, and buildings to crumble. The force of the machine also causes objects to rise and plummet to Earth and buildings to collapse.
As Swanwick contemplates what to do, he receives word that Clark (now being called Superman by some of the soldiers), has a plan. Using the information that Lois obtained, Clark reasons that if the pod that brought him to Earth is activated by the key he has, it will start up the Phantom Drive inside. As well, if it collides with Zod's ship which also has its drive activated, a black hole will warp the ship and the people inside into the Phantom Zone.
Meanwhile, Zod leaves his ship, and heads for the ship Clark found in the Arctic. On board the ship, is a gestation chamber with many unborn fetuses. The projection of Jor-El speaks to Zod, telling him not to do this, but Zod refuses to listen to the words of a ghost, and willing to do what he can as general of Krypton, to revive its civilization and planet. Zod's key eventually overrides Jor-El's, and the ship now responds to Zod, causing Jor-El's hologram to disappear.
Col Hardy, Dr Hamilton, and Lois board a plane to take the pod to Metropolis, while Superman flies around the world to try and stop the World-Builder. However, he is assailed by a Kryptonian defense mechanism within the machine, that attempts to fend him off with long tentacles.
The situation over Metropolis isn't any better, as none of the planes are able to get close to Zod's machine, which has created a gravitational vacuum that keeps the transport unable to properly drop Clark's pod. Realizing there's no way he can fend off the tentacles, Clark goes deep under the World-Builder, and punches his way through it, causing the connection to sever, and the machine to explode. With the gravitational disruption gone, Hardy flies the transport closer to Zod's ship, but it is intercepted by Faora, who attempts to stop them.
As well, Zod has arrived in Metropolis with the ship. As he attempts to blow up the Military plane, Clark swoops in and crashes into the ship's control panel. Zod yells for Clark to once again let him complete his plan to revive Krypton. "Krypton had its chance," yells Clark, who then uses his heat-vision to tear apart the ship, causing it to crash, and the gestation chamber to fracture.
Faora's attempts fail as well, as Hardy steers the plane into the ship. As Lois was on the rear of the plane as it tilted down towards the ship, she loses her balance, and falls off into space. The collision of the two Phantom Drives causes the Military aircraft, and Zod's ship (along with the people on the vessels), to disappear.
Clark manages to save Lois, and puts her safely on the ground. Nearby, the sound of moving metal is heard, and Clark finds Zod, who's thoroughly enraged. Zod tells Clark that he was engineered to be a General of Krypton, and to protect it and its people. With nothing left to revive the planet, Zod seethes that Clark has taken his soul and promises to kill the humans one at a time, in retribution for what Clark has done.
The two then battle across Metropolis, smashing through buildings. During the fight, Zod adapts further to Earth's atmosphere, spawning heat-vision and the ability for flight. The battle soon sends them into a train station, where Zod turns on his heat vision, aiming it at a trapped family. "If you love these people so much, then you can mourn for them," he shouts. Clark begs Zod to stop, but when Zod claims he will never stop, Clark snaps the General's neck, ending his life. It is clear that Clark did not want to exact such a terrible judgement, and he agonizes over having not only killed another person, but one of the last of his race. Lois then shows up and comforts him.
The film then cuts ahead some time later, with Swanwick and Major Carrie Farris (Christina Wren) finding Superman downing a drone. Superman claims that he knows they want to know where he hides, but he wants the searching to stop, and that he'll continue to fight for what is right.
Clark then returns to Smallville, where he and Martha visit Jonathan's grave. Clark claims he wishes his father could have seen what he did, but Martha Kent says he did. When she asks what Clark intends to do now, he claims he'll get a job, where he can be updated on what is going on with the world, and be able to ask questions if needed.
We then see him in the Daily Planet building, being introduced to Lois Lane. Though he is now sporting a pair of black-rimmed glasses, it is apparent (to the audience) that Lois knows just who this new person is.
