It’s the year 2013, and at the
Daily Planet, head reporter Lois Lane reports to editor Perry White. As she goes to her office, she reads a newspaper story about Lex Luthor announcing his candidacy for President. Lois looks for Clark, who has gone AWOL again tracking down a story, and gets word that a news plane is going to crash into the building. She and the rest of the staff run to the window and look out as a heroic caped figure comes to the rescue… and Clark wakes up from his dream, remembering Fate's words that he would lead a new generation of heroes. Looking around, he discovers that his mother has left him a present: a costume with a bright red S on the chest.
Zod, pretending to be the Blur, arranges for a meeting with Lois. She recognizes him as Clark’s supposed FBI agent and friend, and Zod explains that he survived being shot because he has superpowers. Zod speaks of how Lois is his hero and plays along when Lois reminds him that the Blur told her he was ending all contact. The Kandorian says that he needs her help to stop Clark Kent, who is trying to uncover the Blur’s true identity. He warns that Clark hates the Blur because he knows of the close relationship Lois has with the Blur. Lois is skeptical and Zod tells her to investigate for herself to find out that Clark is keeping secrets.
At Watchtower, Chloe teleconferences with Oliver, who is in Washington. She warns him that she hasn’t been able to find the Kandorians, and Oliver insists on returning to help her. He claims that it’s just to protect Watchtower, fooling neither one of them. As Chloe signs off, Clark returns with the Book of Rao. Chloe brings him up to speed, informing him that the other heroes of the team are in the field, armed with the kryptonite weaponry that she and Oliver stockpiled. Clark warns that it’s only a delaying tactic at best given the Kandorians’ overwhelming powers. Chloe prepares to use the Book of Rao to exile the Kandorians to another plane of existence, but Clark informs her that it will affect him as well. He believes that his destiny lies on Earth and he needs to find another way to defeat the Kandorians. However, Chloe wonders if it's a trial and Jor-El has remained silent so Clark can face the test alone. Chloe suggests that his destiny is to lead the Kandorians and go with them to their new home, Clark still insists on trying to save Zod rather than fight him to the death.
Zod goes to the Fortress to destroy the crystal control console. Tess is waiting for him and explains that she's known about the Fortress for two years, and now wants redemption. Zod tosses her aside and admits that his people hid the Book of Rao from him. Tess responds by unveiling a piece of kryptonite, weakening him. She smashes him down and tells him of the future she's seen where Zod destroys the world in his quest for power, and the Red Queen made Tess realize the error of her ways. Zod manages to get clear long enough to recover and use his heat vision to burn her.
Clark goes to the Fortress to speak with Jor-El. He gets no response, and discovers that Zod has destroyed the control console. Zod emerges and notes that Clark can't stop the Kandorians from conquering the plant. Clark says he wants to save him, and Zod wonders if he can get redemption. His opponent notes that he killed Jonathan when he tried to play God, and he's sought redemption ever since. He asks Zod to recall his troops before the battle between the Kandorians and the heroes cause untold deaths, but Zod insists he's fulfilling his destiny and flies away. Clark discovers Tess, her body half burned by Zod's heat vision, and takes her to Metropolitan General for treatment.
Lois arrives at her desk and discovers a priority letter with an air ticket to Nairobi. She then goes to Clark's computer and looks for information on the Blur. One file contains a photo of Zod.
At the hospital, an old woman sits knitting outside of Tess' room. Clark comes to see Tess, who says that she learned the Fortress' location from John Corben when he went there. Clark warns that the console is destroyed and he can't use the Book. However, Tess explains that the Kandorians put a control console in the Sun Tower, and she hid it away atop the church he uses as a vantage point. She warns him that the war has already begun and they've run out of time.
Kandorians across the globe spread destruction in the name of their leader.
At Watchtower, Chloe and Oliver teleconference with their teammates: John, Hawkman, Stargirl, Black Canary, and Cyborg. Chloe says that for now, the military believe it's a hoax, giving the heroes time to deal with the situation since the Kandorians have gone underground. Cyborg and Hawkman suggest aggressive action, but Chloe wants to wait until Clark arrives. They disagree among themselves until Clark arrives and explains that Zod has tricked the Kandorians. He plans to use the Book to peacefully send the Kandorians away, along with himself, and tells them to work together to become a team. They vow to follow his wishes. Chloe walks away and Oliver tells Clark that she's trying to be strong at the thought of losing her oldest friend. He then tells Clark that he has to tell Lois the truth, but Clark believes that telling her his secret just as she loses him will bring her further pain. Oliver tells him to at least say goodbye.
Zod watches Metropolis from the rooftop chapel and Basquat arrives to inquire if Zod has the book. He wonders why Clark hasn't used it to kill them, as Zod has claimed, and Zod insists that he will deal with it. Basquat confirms that they've lured the other heroes to places across the world and destroyed their communication centers, and Clark is alone in Metropolis.
Come the morning, Chloe discovers that they've lost satellite contact with the others. Oliver tries to reassure her and then tells her that he had Queen Industries put a satellite in orbit. He planned it as a surprise gift to her. However, he has to get to the Earth station to establish the connection. Chloe gives him a radio, figuring Zod and his people will attack the station. They kiss and Oliver promises to be careful.
Lois breaks into Clark's loft and goes through his belongings. She finds the journal of Virgil Swann, containing notes in Kryptonian and a sketch of the Book of Rao. Clark comes in and prepares to tell her something before it's too late. He admits that when he went away a year ago, Lois was waiting for him when he returned and that was when he knew she was the one he always needed. Lois tells him that Perry has offered a job at the foreign desk in Kenya. Taken aback, Clark encourages her to go. Lois says Clark is more important than her career, but there can't be ay more secrets between them. Clark insists he doesn't have any but Lois doesn't believe him. He can only hug her and say that her leaving Metropolis is for the best, but he promises to always watch over her. Lois returns his hug and then leaves.
Tess seizes and then dies. Once the doctors leave, the old woman outside goes into her room.
Oliver gets to the satellite station and calls to inform Chloe that he's lost in the ventilation ducts. She directs him to the proper control box and he makes the connection. However, Chloe detects a number of individuals moving toward Oliver. She warns him and Oliver tries to crawl out, but his attackers smash in the ducts from all side. Oliver tells her that he loves her, she says the same thing back, and with his last words Oliver tells her that they're not Kandorians.
Clark goes to the roof of the chapel and finds the console where Tess hid it. He reaches for the Book of Rao in his pocket, but realizes that Lois stole it from him at the barn when they embraced.
Lois meets Zod in the street and admits that he was right about Clark. Zod claims to regret her heartbreak, and promises never to deceive her like Clark did. He asks for the Book and Lois tells him that she hid it at the place where she told the Blur that he was the most important thing in her life. When Zod can't answer it, Lois realizes he's not the Blur. Zod grabs her and throws her toward a nearby phone booth. Clark arrives, smashes him away into the sky, and rescues Lois just in time. When she wakes up, he speeds into a nearby alleyway and Lois sees him in the shadows. She approaches him and asks for his forgiveness. Turning her back to avoid seeing the Blur's face, Lois gives him the Book. Clark then pulls her into his arms and kisses her in the shadows. After a long moment, he speeds away... and Lois says Clark's name.
Cark goes back to the church and prepares to activate the Book. Zod arrives to take it, bringing his soldiers with him. Clark accuses him of cowardice, saying he's hidden the truth. He explains that the Book will take them to a planet where they can build a new Krypton. Clark then talks about Faora, and Zod snaps. He slams Clark into a wall and whispers that he didn't want to kill his unborn child, but Faora didn't leave him a chance. The Kandorians hear his confession with their superhearing and remove their military arm bands. They resolve to deal with Zod when they are on their own soil. Vala asks Clark to take them home.
Clark activates the Book and one at a time, the Kandorians are pulled up into the energy vortex. Zod and Clark are the last to go... and Zod unsheathes a blue kryptonite dagger. Without powers, neither of them ascends. Zod attacks him and they struggle, smashing through a window into the chapel. They fight to the ledge and Clark lets Zod stab him. He falls backward into space
Vala and the others ask Clark to take them home, and Clark places the Book in the console. A burst of energy flares up into the sky and the Kandorians are pulled up into the light. However, Zod reveals his trump card: a dagger of blue kryptonite, which renders both him and Clark powerless non-Kandorians, immune to the Book.
The two men fight without their powers. Clark vows not to let Zod destroy his second home, grabs the knife, and pulls it into his chest. As he plummets backward, the blue kryptonite dagger falls with him. Zod is banished from Earth by the Book, while Clark plummets to his death...
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