第六季故事为第五季结束时，萨德侵占莱克斯的身体，并灌输他跟克拉克一样的超能力，还释放一种病毒到地球。
This episode begins with the following story lines in play: Zod has taken over Lex's body as his vessel and convinced Lana to meet him on the roof of LuthorCorp, Chloe and Lionel are stuck on the streets below amongst the rioting. Brainiac has unleashed an electronic virus that has wiped out the worlds power, and has also taken over the LuthorCorp jet carrying Martha and Lois, unconscious from lack of oxygen, to an undisclosed location. Clark has been sent the Phantom Zone, trapped in the Kryptonian prison that he inadvertently freed Zod from.
Somewhere in space a Kryptonian prison, created by Jor-El, holds Clark. He lands on the other end, in unfamiliar grounds, where he's attacked by a phantom when a woman appears and banishes it with a stone, kicking Clark in the face and welcoming him to the phantom Zone.
Back on Earth Lionel is fighting off the angry rioters that have pulled him and Chloe from his Limo. One of his security guards says they need to get off the streets and that Lex is already inside. Lionel sees Chloe being pulled away and the security guy ensures that he will get her.
On the roof of the LuthorCorp building Lana tells Alex/Zod that the city is tearing itself apart and they must help them with the powers Fine gave him. He informs her that Lex Luthor is dead and that his name is Zod. Lionel and Chloe arrive on the roof just as Zod flys off with Lana. Back inside they realize that Clark must not have been able to get to Lex and stop him before Zod took him over. Lionel knows that Jor-El gave Clark a dagger and says he will go back to the Kent farm to retrieve it because it may be what can stop Zod. Chloe is surprised that Lionel will resort to killing Lex and suggests they try to read the Kryptonian symbols in an attempt to shut down the virus. Lionel knows that Clark is the only one who can read them. He says the connection he felt to Jor-El and the Fortress is gone. Chloe has injured her leg and can't make it back to Smallville so Lionel gives her a gun, tells her to take care of herself, and leaves for the farm.
Clark awakens to find himself in a tent with the mystery woman who demands to know where he's from. Clark informs her he was born on Krypton and raised on Earth. She calls him Kal-El and says she knew his father.
Zod takes Lana captive and drags her to the black ship. She realizes that Lex has been taken over and tells Lex that he needs to fight this. Zod tells her Lex is dead but she refuses to believe it. Lana watches as Zod touches the ship and makes it disappear in a flash of light leaving the only a Kryptonian device in Zods hands. He tells Lana that she will bear witness to the end of the human era and the rebirth of Krypton, and that she will have the privilege of playing a part in its resurrection.
Martha awakens amongst the ruin of the jet, having crashed in the snowy mountains, and finds Lois unconscious and injured. She enters the pilots cabin, finding all the electronic equipment fried and burnt out, unable to get a response on the radio to her mayday call. Martha peers out the front windshield to see they have crash landed in front of the Fortress of Solitude. Martha drags an unconscious Lois to the Fortress and has her first conversation with Jor-El. She accuses him of crashing their plane, but he explains that she was, in fact, taken by Milton Fine and he saved them. He tells her that Clark is banished forever by Zod. He tells Martha about the dagger he gave Clark and how Zod must be stopped and killed in order to save the world. He thanks Martha for being such a good mother for his son and transports them back to Smallville.
Raya cleans Clark's wounds as he has no powers where they are. She explains that Jor-El founded the Phantom Zone as a prison for Kryptonians as well as intergalactic criminals from the "28 known galaxies". Raya tells Clark that most vicious offenders are condemned for eternity, they lose their corporeal bodies and become Phantoms, and that a crystal Jor-El gave her is her only weapon against them. She says she was one of his father's assistants but as Krypton was being destroyed, Jor-El put her in the Phantom Zone for her own survival. His father and mother didn't come with her because Jor-El wouldn't stop trying to save Krypton and his mother wouldn't leave his side. Clark tells her that Zod has returned to Earth, because of him, and he must go to stop him. He asks if there's a way out since she helped his father create this place. Raya says that Zod is a soldier and will only kill Clark but he says it's worth the risk to save everyone he loves. Raya tells him he truly is his fathers son.
Chloe goes back to the Daily Planet to try to decipher the symbols. She's startled when she hears someone else in the building and starts firing shots. A guy appears, insisting he works there and is surprised to see its Chloe. Jimmy Olsen, the photographer with whom she had a summer romance with while in high school, smiles and asks this isn't cause I didn't call you back right?
Zod brings Lana back to the Luthor mansion and she insists that there must still be a part of Lex inside him if he remembers this place. He tells her that he's only there because the virus that's crippling earths technology can only be stopped at the original point of infection. He tells her that he intends for her to bear him an heir and begin his plans to turn Earth into a Krypton-like planet using the alien ship's hard drive. Lana tries to stop Lex/Zod and he keeps her in place by pinning her hand against the wall with a knife. He leaves to infiltrate the Pentagon, where he plans to control Earth's satellites. When he leaves, Lana is able to pull the knife out and free herself.
Back in the Phantom Zone Clark and Raya are making their way to an exit out of the Phantom Zone, a gateway designed by Jor-El in case anyone in his family were imprisoned there. Raya explains that only a member of the House-of-El can open the gate when they are suddenly attacked by Nam-Ek and Aethyr. Nam-Ek gets a knife to Clark's throat, insisting on killing Clark for sending him there, but Raya implores Nam-Ek to stop. She says she was bringing Clark to him since he is the only one who can open the gateway and free them all.
Lionel shows up at the Kent farm happy to see Martha there and unharmed. Martha try's to explains about Lex but Lionel says he knows what he must do. Lana also arrives, looking for Clark and having realized now why Clark was talking to Chloe about killing Lex. Lionel asks Lana where Lex is and but she says that with the things he can do now nobody can stop him. Martha shows them the dagger and says she can kill Lex with it. Lana reasons that she is the only person that would get close enough to use the dagger and offers to kill Lex.
She takes the dagger back to the mansion, where Zod is waiting. She tells him that she has agreed to bear his heirs and they start kissing. Thinking he is distracted, she tries to stab him, but he is too quick, kicking Lana across the room Zod shatters the knife. Angry, he uses the hard drive to activate a satellite which shoots a ray of light back down to Earth.
At the Daily Planet Jimmy Olsen is telling Chloe it was his first day of work there when suddenly an earthquake begins. Chloe saves Jimmy from a TV as things start crashing down around them.
Clark and Raya make it to the gateway with the two prisoners, Aethyr and Nam-Ek. Raya says they need Clark's blood to open the gateway as he says he trusted her. Nam-Ek says trust is for the weak. Raya suddenly slashes Nam-Eks throat and Aethyr retaliates, fighting back with Raya. She urges Clark to get to the gateway to escape, he runs to the portal, placing his bleeding hand on it. As the portal opens, Raya is stabbed and a pulse of light pushes Clark and a few other prisoners through.
Seven meteor-like objects fall from the sky out of the Phantom Zone, one of them being Clark. He arrives at the farm just in time to save Lionel and Martha from being crushed by the collapsing barn. Clark asks Lionel and Martha where is "he"?
At the mansion Zod throws Lana against the wall telling her she could have been at his side but now she will die with the rest. Before Zod can choke Lana to death, Clark arrives. He blasts the hard drive with his heat vision which deactivates the satellite and stops the earthquake. They fight and Zod picks Clark up and flies out the window with him. They land in a forest and battle. Zod says he doesn't know how Clark escaped the Zone but he was safer there. He gains the upper hand and hurtles Clark out to a field. Clark says he won't let Zod destroy Earth like he did Krypton but Zod says Jor-El couldn't stop him, neither will his son. He's disappointed but tells Clark that if he swears his allegiance, he will spare the humans lives that Clark cares so much about. He commands Clark to kneel before Zod. Clark appears to accept his offer and takes Zod's hand. However, in his hand is Jor-El's emblem from Raya. Zod is sucked out of Lex's body and into the emblem while Lex falls unconscious.
Clark goes to the hospital to check on Lois, who doesn't even remember the plane going down. She says she remember the cabin losing pressure, gasping for breath and then suddenly being in a palace of ice, bathed in warm light. Clark tries to convince her it was just a hallucination but she insists it was real, claiming she thinks she died and went to heaven. They share a tender but awkward moment. Lex encounters Lana in the hospital and she is understandably skittish towards him. Lex tells her he remembers being in the field with her and then everything going white, next thing he knew he woke up in the hospital. He notices Lanas wound on her hand, where Zod stabbed her, and asks if that's why she's afraid of him. Lex seems sincerely guilty over having caused such destruction. Lana insists he wasn't himself, that she tried to stop it and admits to almost having killed him. Lex says he would have done the same thing and vows to try and rebuild everything he damaged. Lana tells him that it might not be that easy.
Clark goes to the Daily Planet to check on Chloe, who was extremely worried and is relieved to see him. Clark asks if she's ok and Chloe says she is now that he's there. As they embrace, Clark gets uncomfortable and he tries to bring up when she kissed him, but Chloe blows it off saying it was the end of the world and she's not expecting them to hook up. Clark awkwardly agrees that he doesn't with. Just then Jimmy Olsen shows up and as Chloe makes introductions there seems to be an weirdness between Jimmy and Clark. Clark notices the way Chloe is acting with Jimmy, picking up on the obvious connection between the two. Chloe and Jimmy go off to get something to eat as Clark is left behind, looking a little confused and bewildered.
Back at home, Martha tells Clark that Lionel claims his connection to Jor-El is gone. Clark tells her that he took Raya's crystal to the Fortress for safekeeping and tried to talk to Jor-El, but he wouldn't answer-that the Fortress was dead. He confides in his mother that he doesn't know where to go from here... everything has changed. His father is dead, Jor-El is gone, Lex has become his enemy and Lana won't speak to him. Martha tells him to follow his heart and he'll always do the right thing. Clark says that he thinks Kryptonians must have thought the same thing because Jor-El sacrificed himself to save Krypton and Raya died saving him. Martha says that every world needs their hero's.
Meanwhile, Lionel is at his office, writing Kryptonian symbols; he suddenly seems astonished that he understands something and writes "POWER" underneath one of the symbols. Lex returns to the mansion and opens his laptop to find a part of the device Zod had taken from the ship, half destroyed.
In Patagonia, Argentina, a phantom rises from the waterfalls and speeds away.
