We open over the roaring fury of Rao's surface, and the glint of a space station just above the stellar maelstrom. The station is peppered with impacts from micrometorites, but looks like some ancient temple adrift in the void. A decrepit communications antenna adjusts its position and prepares to transmit, and we pan over the star system to reveal an ancient world dotted with city lights and ringed with the debris of eons worth of space exploration. We see the heart of Krypton, the City of Kandor, a monument to an age gone by, wet and tarnished beneath a red-orange sky, but still a symbol of a once great civilization.
The film cuts to the House of El, and we see Lara Lor-Van over the crib of the infant Kal-El. Jor-El enters, visibly exhausted but dignified, expressing to his wife how the prolonged sunspot activity has made the days of Krypton more taxing. He returns to his study with grey slates revealed to be interfaces of some kind, and pours over holographic data. Lara expresses concern for Jor-El's research, and fears the High Council would sooner bury her husband's findings than act on them, Jor-El simply hopes he won't be ignored as he has before. The following day Lara's fears are realized, and we see an ignorant and corrupt High Council of Krypton, who patronize Jor-El's work, or question some of the very notions behind his theories. They defer constantly to Braniac, who only affirms their ignorance. Jor-El states that Rao will go Supernova in a matter of weeks, and urges the Council to prepare for an evacuation. He is cast out of the council chambers.
Jor-El returns home, defeated, only comforted by his wife and the sight of his son. He returns to his lab and works to complete the lifeboat his son. A small craft, cobbled together from the remains of the once great fleet of the Kryptonian Imperium. The following morning, Lara tearfully swaddles her child in the ancient red pennant of the House of El, and Jor-El places his son in the capsule with a small black box. As the hatch closes, the cabin places the child in a state of suspended animation and lifts off as Jor-El and Lara embrace eachother. As the ship leaves the system we watch Rao begin to flicker and explode in a great supernova. As the opening credits roll we watch the shockwave vaporize worlds, send ships careening off course, and in once case we see the green shield emanating from a man fighting against the wave collapse and the glint of a green speck drift into the void. Finally, in 1938 the ancient capsule reaches the Earth and falls into the atmosphere. We see a young John and Martha Kent stargazing in the back of John's pickup, when a shooting star races across the sky, and is followed by a sonic boom, then a crash; the camera holds on the same spot of the sky as the Kents drive off, and we see one red star go out. Fade to black.
Cut to 1954, Kal-El is now Clark Kent, age 16, and attending Sunday services with his parents, accompanied by Lex Luthor, a boy who grew up on the wrong side of the tracks. We see the two boys as close friends, and Lex a welcome guest at the Kent house. As the group exits the local Methodist Church of Smallville, Clark runs off to meet Lana Lang, while John and Martha happily look on and Luthor tries to hide his jealousy. Lana and Clark flirt back and forth at a local diner before Lana leaves in a panic after realizing she's late for something. Clark leaves the diner and enters into the alley just behind the building. He looks both ways, smiles and flies into the air. We are treated to a flying scene that shows the joy Clark gets out of his powers. The next day Clark and Lex return to Smallville High, and we see Clark as both honor student and captain of the football team. We only see shadows of the boy's great and growing power in the way he plays the on the field. Clark waves to Lana from practice, Lana is in the chemistry lab when a sonic boom cracks the sky and shakes the Earth, causing the lab to suddenly bursts into flames. Clark runs in at tremendous speed and we see fire dance around his flesh without burning it, as he pulls student after student out of the inferno, eventually rescuing Lana. As he exits a crowd has formed of other students and faculty, all trying to help revive the other students. Clark's coach approaches the boy calls the boy a hero, but we see many people look suspiciously at his lack of burns, some look almost frightened. Clark is visibly shaken by the way people look at him, and he hears their whispers as a cacophony of mistrust. Lex tries to congratulate him before he runs off.
Upon returning home Clark nervously tries to make dinner, still having trouble dealing with the way his friends and neighbors looked at him earlier. His mother comes in and tries to talk to him before panicking at the sight of Clark's hand on the stovetop. He removes it, undamaged, and begins to silently sob, asking, "what am I?" John enters the room and Martha gives him a look of concern, and knowing that the day they dreaded has come. The Kents take Clark to the tornado shelter beneath their home and John reveals to Clark a dusty footlocker. Clark sees its contents before Johnathan ever opens it, but is confused as to its significance. It his here that the Kent's reveal to their adoptive son his true origins. Little remained of the ship he arrived in, a few scraps of metal, the red pennant with a golden shield , and a black box with a simple message from his true parents. Clark holds the box and a message that only his ears can hear and his eyes can see plays. Jor El and Lara speak of Krypton, his birthname, and the legacy of their people, stating that under the light of Earth's yellow sun, he is everything their race once was, and closes with their love. Clark calmly hands the box back to his father and embraces his parents.
Cut to a grove of Hickory trees along a river and we see the impact site of the object that caused the sonic boom from earlier. A deer walks into frame and a single light begins to flicker on the strange object, the deer runs away and the stillness of the forest is awash with animals fleeing from the object. Its obsidian black undercoat is trimmed with a crystalline material and an untarnished metal. Beneath the crystal of the object's face, we see three glowing green circles.
Back at their high school, Lana looks for Clark on the Football field, but is informed that he quit the team, claiming his heroic efforts have left him having trouble breathing and nearsighted. Lana finds him in the Journalism club, bespectacled and talking to Lex about doing a piece on the Soviet test of a Hydrogen Bomb. Lana confronts Clark, who begins to cough almost on cue, and thanks him for saving her life, granting Clark a kiss in front of Luthor, who nervously tries to change the subject to the sonic boom that caused the chemistry lab to explode. Lana leaves, asking Clark to meet her after school, and Clark looks at a story about local dogs and cats disappearing from the town of Lyons, and a reported explosion just outside of the town just a day earlier. The same day as the Chemistry Lab fire. Clark and Lex look at eachother and we cut to the two driving to Lyons, Luthor is driving his father's old Buick, and Clark is nervous about Lex "borrowing" his old man's car, Lionel Luthor being known as an abusive drunk. Lex shrugs off his friend's concerns, saying that he's smart enough to keep his old man from finding out about their little excursion. The two meet several locals who direct them to a crash site, Clark dutifully writing down their testimonials.
They reach the grove and the crash site, revealing the object. Clark has been complaining of a shrill noise for the last leg of their journey and his holding his ears as Lex approaches the object. Lex is fascinated by the object and remarks about how small the impact crater is and how such a thing that could break the sound barrier and crash could be so undamaged. The ringing in Clark's ears is now at a fever pitch before it abruptly cuts off and the three circles glow green. A voice emanates from the object, "Seeking the codex of Jor-El." A force knocks Luthor on his back and the craft rises into the air. It flies off toward Smallville, Lex gets up, but is limping. Clark tells him to drive to Smallville to warn the town while Clark will find help in Lyons. Lex drives off, and just as he is out of site, Clark puts his glasses away and leaps into the air. He races after the object, knowing exactly where its going, and in a matter of minutes Clark catches up the craft, which stops midair. The voice asks the boy to identify himself, intrigued by the flying being on this primitive world. He gives his Earth name, and asks what the object is and what it wants. The object reveals itself to be Braniac, the construct that served as Kyrpton's custodian AI, who saved himself rather than the people of Krypton, who Braniac viewed as inferior shadows of a once great civilization. The Codex of Jor-El contains all of Jor-El's research, and is one of the few repositories of Kryptonian knowledge Braniac does not control. He further states that after downloading the content of the codex, he use the Earth to create a new Krypton by destructive means. Clark attacks the object which unfolds into a skeletal humanoid. The battle rages across the sky, and Braniac upon touching Clark discovers him to be Kal-El. He attempts to reason with the boy, speaking of his birthright as the last Kryptonian. Clark proudly proclaims himself to be the son of Earth, and punches Braniac into the dirt. He lands, and we see Braniac's body broken and in pieces. Clark puts his glasses back on and feigns exhaustion from running to see the impact when several police officers come nearby. Clark proclaims himself to be a reporter for the Smallville Highschool paper, and the two officers shoo him away. Clark returns home to greet his parents, he tells the story and the Kents suggest that maybe he is meant to be Earth's protector.
The next day Lex is in the journalism club's room passed out, when Clark enters. He wakes, revealing a black eye, saying that his father knocked him out when he got back to town, and he was unable to warn anyone about the incident in Lyons. Clark assures him that there was no danger after all, and the object fell out of the sky shortly thereafter. Lex nervously states that the object is clearly from another world, and is by definition a threat to this one. Clark once again gets nervous at this xenophobia, but before the argument can continue Lana rushes in while a collection of other students storm down the hallway to the teacher's lounge. There the radio is playing a broadcast about how the police station in Lyons was suddenly destroyed by a mysterious figure, and unconfirmed reports of an object from the station flying towards Smallville. Lex looks at Clark with an "I told you so," glare. Braniac is self-reassembling en-rout to Smallville, meanwhile Clark leaves the school and flies for home. He lands, shocking his parents, and warning them to get out of the area before Braniac fires a volley of energy at Clark, dropping him. Johnathan emerges with a shotgun and knocks the machine over with two shots. As he reloads the machine rises again with only scorch marks on his crystalline Chest. He demands the codex and grabs the shotgun from Johnathan just as he fires again. Martha is knocked to the ground and Johnathan is held aloft by the machine. Braniac thanks Johnathan for caring for the Last Son of Kyrpton before he is grabbed from behind and thrown across the farm by Clark. Braniac rises again, his body self assembling, and remarking that Kal-El could rule this world as Krypton is made anew. Clark responds with a punch that knocks the robot head first into the ground. Braniac's head reassembles to the left of Clark's fist as his arm punches him the ribs, knocking him back to his parent's porch. Martha is holding John who is clutching his injured neck and Braniac states that at the very least, he can use Clark's genetic material to create a new race of Kryptonians. Clark rises to fight Braniac again throws a great punch, only for him to miss and Braniac to grab hold of his face. The machine muses to the Kent's about the greatness of the ancient Kryptonians when we see the back of Braniac's hand glow red before being sliced apart by Clark's heat vison. The machine attempts to reconstitute itself as Clark uses another blast to cleave the bore a hole down the length of Braniac's body. With the fight over, Clark embraces his parents. Fade to black.
Cut back to Smallville High, the cover story of the school newspaper boasts a story by Clark about the crash landing of a mysterious object outside of Lyons, declared by the government to have been a weather balloon. The camera pans over Clark laughing with Lana and Lex in the Journalism room, and we are treated to a photo montage of Clark's high school graduation, college dorm life, inter-spaced with news clippings of sightings of a mysterious blue and red figure. We then cut to 1966 where Clark gets a job as an intern at the Daily Planet. He's clumsily carrying papers between the desks of Journalists before spilling Perry White's coffee. Perry exasperatedly tells Clark to go on his lunch break before he hurts himself. As Clark walks down the sidewalk of Metropolis the sound of someone screaming echos across the city, and Clark runs into a telephone booth where he opens his shirt to reveal the iconic Superman S. Credits.