Trapped within the Phantom Zone crystal, Clark looks down towards Earth helplessly. He smashes his fists against the crystal but to no avail. The floor gives way and Clark falls by strange crystal formations and eventually into an open desert-like area, tumbling down a grey sand dune. He picks himself up to find his lip bleeding. Wandering around the barren landscape, some kind of being flies past. Clark calls out to see if anyone is there but no-one answers. The being returns, it's a phantom and starts to attack Clark. His face begins to bleed and more phantoms join in as he's dragged across the floor. A veiled figure appears holding a crystal that emits a powerful beam at the phantoms who quickly disappear. Clark offers his thanks and the figure swiftly kicks him in the face, knocking him unconscious. The figure pulls down its veil to reveal a beautiful woman's face. "Welcome to the Phantom Zone," she says.
Lionel is beaten by a group of men as riots rage through Metropolis. He sees Chloe in the distance being hauled away by a man and decides to intervene. He fends off his attackers and makes his way towards Chloe, taking out anyone that gets in his way. A rioter grabs Lionel from behind and starts to choke him before Lionel's bodyguard pulls him off. He tells Lionel he needs to get inside and that Lex is already there. Another man is pulled of Chloe and she makes her way to safety with Lionel.
Lana looks on from the rooftop of LuthorCorp as smoke billows out in the distance. She pleads with Lex to save the city using his new found powers that Fine gave him. He responds that Lex Luthor is dead and his name is Zod. Lionel and Chloe arrive on the rooftop just in time to witness Zod flying off with Lana.
Lionel and Chloe plot to stop Zod with the dagger given to Clark. Chloe offers to find out about the virus tearing the city apart and maybe she can match up the symbols. Lionel admits it's useless as they need Clark to decipher them. His connection with Jor-El at the Fortress of Solitude is gone. He can't feel his presence anymore. The only thing they can do is get to the dagger and stop Zod. Chloe can't make it back to Smallville with her injured leg so Lionel hands over his gun before taking off. Chloe wonders where Clark is and could really use his help right now.
In the Phantom Zone, Clark wakes up inside a tent. The woman that saved him earlier kicks him in the stomach and holds a knife to his throat asking him where he's from. Clark tells her he was born on Krypton and raised on Earth. She realises who this may be, "Earth? Kal-El?" Clark asks her how she knows his Kryptonian name and she tells him she knew his father. She opens her palm to reveal the crystal that had saved Clark - it has an S on it.
Zod takes Lana inside a warehouse and shows her the black spaceship. He takes a handheld device from the ship and it disappears.
On a snowy plateau, Martha regains consciousness and surveys her surroundings. She finds Lois near the back of the crashed plane and covers her with a blanket to keep her warm. Martha enters the cockpit to discover no pilot there. She tries to call for help on the communication system but her gaze is drawn to something outside. In the distance, she sees a crystalline structure - it's the Fortress of Solitude. She drags Lois there on a makeshift sled. Martha asks Jor-El what happened to Clark and he explains that he's been banished forever by Zod. Martha tells Zod to bring him back but it's not within his power. Clark's destiny is now his own. Jor-El tells Martha that she must complete his task, to retrieve the dagger and kill Zod's vessel, Lex Luthor, in order to save everyone. She agrees to the task and asks to be sent back. Jor-El offers his deepest gratitude to Martha for guiding his son and sends her back to Smallville in a flash of light.
Back in the Phantom Zone, the woman that helped Clark reveals her name to be Raya as she tends to his wounds. She tells him that the Phantom Zone was created by Jor-El to hold prisoners whose corporeal bodies are destroyed and their essence haunt the wasteland. Raya was an assistant of Jor-El's and he sent her to the Phantom Zone because he thought she'd have a better chance of survival there. All she has left of Clark's father is the crystal around her neck. "Every day, he still saves my life." Clark stands up and tells Raya he needs to go and stop Zod. There must be a way out of the Phantom Zone.
Chloe is under a desk at the Daily Planet trying to decipher the Kryptonian symbols when she hears a noise. She takes Lionel's gun and peers out. She hears another noise and shoots. A young man steps out telling Chloe not to shoot, he works here. He recognises her and asks if this is because he didn't call back. Chloe knows who this is, it's Jimmy Olsen.
Zod and Lana arrive at Lex's mansion. Zod tells Lana that Lex's feelings for her were strong and left an unpleasant taste when he consumed his essence. He reveals that the virus can only be stopped at the point of origin and that's why he's here. He restores the computer systems and tells Lana he needs the Pentagon satellites to help reshape the Earth's crust and make it the new Krypton. Lana pulls out a fireside poker and tells Zod she won't let him do this. Zod calmly takes the poker and forces it through Lana's hand and into the wall. He tells her they'll discuss this later and leaves. Lana manages to pull the poker out of the wall and her hand as she screams in pain.
Clark and Raya walk out into the wasteland as Raya explains the gateway to leaving the Zone. It can only be opened with the blood of the House of El and was created in case anyone wanted to imprison Jor-El's family. Suddenly, a shuriken strikes Raya in the arm as two figures ambush Clark and Raya. One pulls off his hood to reveal his identity, it's Nam-Ek, who had been sent to the Zone by Clark. He pulls out a knife and prepares to kill Clark but Raya stops him. She says Clark can open the gateway and that she was bringing him to Nam-Ek. He can free them all.
Martha picks up the dagger at the farm and is soon joined by Lionel. Lana also arrives and Martha explains that Zod needs to be stopped with the dagger. The only person that can get close enough to Zod now is Lana and she volunteers to kill him with it.
Zod returns to Lex's mansion to discover Lana has escaped. However, she walks in behind him and admits running is pointless. She agrees to give Zod a heir, the first of many and they begin to kiss. She pulls out the dagger from the couch and attempts to stab Zod but he calmly grabs her arm saying, "You shouldn't play with things you don't understand." Zod throws Lana across the room and snaps the dagger into pieces. He accesses a Pentagon satellite which begins to send a pulse to start changing the Earth's crust.
At the Daily Planet, everything begins to shake and a piercing sound forces Chloe and Jimmy to cover their ears. Chloe pushes Jimmy aside just in time as a television drops above him.
Raya cuts Clark's hand with a knife and states the blood of the House of El is the key to open the gateway. Clark tells Raya he trusted her. "Trust is for the weak!" Nam-Ek responds. And with that, Raya spins around and slices Nam-Ek's throat. She fends off his companion and tells Clark to use the gateway as other prisoners of the Phantom Zone arrive. Clark places his hand on a pedestal with the symbol S on it and activates the gateway just as Raya screams out in pain having been stabbed. Clark disappears in a flash of light.
Clark lands back on Earth, creating a large crater and runs back to the farm.
Martha and Lionel are in the barn where things are falling all over the place. A large wooden structure falls down towards them but stops at the last moment. It's Clark who is holding it up and he asks where Zod is.
At Lex's mansion, Zod picks up Lana like a rag doll and starts to strangle her only to be stopped by the arrival of Clark. Lana falls to the floor unconscious. Zod cannot believe his eyes. Clark uses his heat vision to destroy the handheld device spinning on the Pentagon computer which stops the satellite pulse. Zod rushes at Clark and they smash a window as they spin through the air before landing in the woods. Zod repeatedly punches Clark and throws him through the woods into a field. He orders Clark to swear his allegiance to Zod and he'll allow his loved ones to live. Clark reluctantly kneels and Zod holds his hand out. Clark grabs Zod's hand who begins to smile but that quickly changes as a light emits from the pair's hands. Zod draws his hand back and opens it up to reveal the crystal that Raya had shown Clark previously. Zod screams as his essence is absorbed into the crystal and Lex falls unconscious. Clark picks up the crystal.
Clark visits Lois at hospital. She describes her experience at the Fortress of Solitude and thinks she died and went to heaven. Clark dismisses it as a hallucination. He holds her hand and tells her he's glad she's back.
Lex finds Lana in the hospital and wonders what happened. The last thing he remembers was being in the field with her and after that, he woke up here. Lana tells him he wasn't himself when he caused all the damage.
Clark reunites with Chloe at the Daily Planet. He uncomfortably brings up the subject of the kiss before he left and Chloe assures him it was nothing. Jimmy appears and Chloe introduces him to Clark before they leave him to grab something from the vending machine.
On the farm, Clark finds his mother tidying up in the barn. He tells her he took Raya's crystal to the Fortress of Solitude for safekeeping and tried to talk to Jor-El but there was no response - the Fortress is dead.
Lionel is scribbling down some Kryptonian symbols and writes the word 'power'.
At his mansion, Lex opens a case and pulls out a fragment of the handheld device Zod had used.
At Iguazú Falls in Patagonia, Argentina, something flies over the water and up the waterfall. It's a phantom from the Phantom Zone.
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