When the film starts, Clark Kent, 28 has been in Metropolis for 3 weeks after getting a job at the Daily Planet and has been cleaning up the streets at night time after working throughout the day as Clark Kent without a costume. He is paired with bottom end reporter Lois Lane as the two are looking around for a break through story. Lois thinks she is onto a winner in the suspicious Lex Luthor and his ties to Intergang, Metropolis' premiere mob. Lex has been paying Intergang to destroy the reputations of his rival companies and cripple them financially so he can get there contracts and make LexCorp even richer. John Corben is the top reporter at the Daily Planet and is working for Lex keeping him up to date on Lois' report on him and helping him keep a clean image within the Daily Planet. Lois begins to notice that the crime rate in Metropolis has dramatically fallen in recent weeks and begins researching about a mysterious savior spotted hundreds of times with seemingly supernatural powers.
Clark is struggling to work out how to fully help Metropolis and the world whilst still protecting his parents. He goes to visit them in Smallville to discuss his future and they say they told him to hide his special powers and stay away from the public eye. Clark though is adamant that he can't sit back any longer and do nothing. His parents give in and say that if he wants to expose himself they can do nothing, so they decide he needs a seperate identity in case they are implicated. Martha gives him the blanket he was wrapped in when they found him for inspiration and creates a blue and red costume with the blanket acting as a cape. Now armed with a seperate identity, he makes a full assault on the criminal underworld and soon everybody is talking about the mystery savior with the internet going crazy and all the media bidding for an exclusive interview.
Lex Luthor meanwhile has paid Intergang to kill off Lois Lane who is getting closer to tieing him to the mob. When Lois leaves work one night she gets a cab which is driven by a Intergang hitman and and is kidnapped and taken to Metropolis Docks to be killed but before she is, Clark who super hears from the Daily Planet changes into Superman and saves her and trapping the hitman inside the cab leaving Lois in love. Agreeing to give her the exclusive interview, she dubs him SUPERMAN and is made a superstar reporter overnight. With a name for the mystery savior and a story, Lex Luthor sees this as the opportunity to have his own super soldier and creates a fake hostage situation at his own office to draw Superman in and offer him a position as his security, but Superman refuses saying he doesn't work for criminals and secretly tapes Lex revealing his links to Intergang. Feeling insulted Lex has Intergang kill Superman. Back as Clark Kent, he leaves the recorder with Lex's testimony on Lois' desk as a note from Superman and she exposes Lex to the world as a crook in the Daily Planet. Lex is arrested and questioned over the testimony before making bail. Intergang again kidnap Lois to draw in Superman and use all there force to try and destroy him but to no avail. As Superman ties them all up, they are interupted by the the sudden arrival of a Skull Shaped ship above Metropolis and Brainiac, an android alien who has come to earth in search of the Crystal of Knowledge. Recognising Superman as a Kryptonian and the owner of the crystal, he threatens to destroy his adopted world unless he hands over the crystal. Superman who believes he is human has no idea what Brainiac is talking about. Angered by his response, Braininac begins attacking Metropolis forcing Superman to engage Brainiac while the national guard and armed forces led by Lois Lane's father Gen. Sam Lane attack his ship that is attacking the city. After Superman destroys Brainiac, his ship is left defenceless and the army destroy it sending it crashing into Delaware bay but not before Brainiac shoots an escape pod containing his programming out. With Superman a worldwide hero and the seeming threat of Braininac gone, Superman extends his barrier of protectivity worldwide to the far reaches of the planet.
Brainiac meanwhile, identifies LexCorp as a potential candidate to build him a new body. Confronting Lex and offering him the knowledge of how to kill Superman in exchange for building him a body, Lex agrees and is given designs by Brainiac to follow. After gathering the materials for his body, including an artifical metal called "METALLO", Brainiac takes control over LexCorp's machines and begins assembling his new body and creates a duplicate body. Once completed, he observes Superman from a far to gain knowledge about his life and observes his dual identity as Clark Kent/Superman. Now with the knowledge that he is Clark Kent, Brainiac kidnaps his parents Jonathan and Martha as well as taking Lois Lane to the top of LexCorp's building. Calling out to Superman, he has the choice of choosing to save either his parents or his friend unless he gives Brainiac the Crystal of Knowledge. Imploring Brainiac that he doesn't know about the Crystal of Knowledge, Brainiac goes to shoot Martha Kent but Jonathan steps in front and takes the bullet. Angered, Superman attacks the primary Brainiac and a brutal fight ensues. Brainiac's duplicate engages Superman also and a fight throughout Metropolis breaks out which then the military get involved in again led by Gen. Lane. Taking control over their vehicles to use them against Superman, Lex Luthor looking to redeem himself in the public eye armors up in his own personal Power Suit and helps Superman defeat the 2 Brainiac drones. Returning to LexCorp tower to see his father lying dead in his mother's arms, Superman holds back the tears to avoid comprimising his identity before fleeing. With the world still in amazement at the alien battle right in front of their eyes, a small funeral is held in the town of Smallville as Jonathan Kent is buried in a small memorial service.
After the wake held at the Kent Farm, Martha admits the truth that Clark is an alien and that his ship is buried in the back quarter cornfield. Digging it up, he finds the Crystal Brainiac was looking for and takes it to the arctic circle and buries it away from civilization. Just as he is about to leave, it begins to grow into a building creating the Fortress of Solitude. CUT TO BLACK
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