Clark is working in the barn and a mysterious wind and reflecting light appears. At the Luthor mansion, Lex Luthor and Lana Lang are sleeping on the couch together and Lex starts acting strange and has a pain in his head. He takes off in his car driving fast with Lana following him. Lex pulls over by a field and starts running through the field with Lana chasing him. He comes out into an open area and the pain subsides, he warns Lana to stay away. The ground starts erupting at his feet all around him. Just then a shadow falls over Lex and Fine appears next to Lana. Just then a beam of light comes down from a spaceship and takes Lex up into it. The ship leaves a kryptonian symbol on the ground and disappears.
At the Kent Farm, Lois is on the phone with an airline company trying to get a flight for her and Martha to go to Washington. Lionel comes by and offers to take them in the LuthorCorp jet. She declines and Lionel starts complimenting Martha on her rare qualities and is quite close to her.
Lana visits Chloe at The Daily Planet and she tells Chloe about Lex being abducted by the black spaceship. Fine was there and Lana blames herself for getting Lex involved. She is worried that Lex is dead.
Chloe visits Clark at the barn and tells him about Lex’s abduction. Clark is thinking that Zod is using Lex to get himself free. Clark tells Chloe that he needs to go talk with Jor-El about this. He goes to the Fortress of Solitude. Clark talks with Jor-El about how Fine is back and how they can stop him. Jor-El tells Clark that the ship and Fine are preparing for Zod to come back. Zod is imprisoned in the Phantom Zone and that he killed him and his mother. Zod’s physical body was destroyed, but when Zod is released he will need a new physical body. Jor-El gives Clark a kryptonian knife to kill Zod’s human form when he returns, whomever Zod inhabits.
At The Planet, Clark has returned and is talking with Chloe about having to kill Zod. They don’t know who it will be, but that it might be why Lex was captured so Zod can inhabit his body. Clark then states that if it is him, he will have to kill Lex. Lana overhears the last statement of how Clark has to kill Lex from the doorway.
At the Kent Farm, Clark pulls out the knife from where it is hidden. Lionel walks in an sees him with it. Lionel asks what Jor-El wants him to do with the dagger. Lionel brings another paper with kryptonian symbols, Clark translates it as “Sacrifice The Vessel”. Lionel wants to help him, but Clark tells Lionel about he will have to kill the vessel. Zod will inhabit a vessel that Clark will have to kill. Clark says that he can’t kill anyone. Lionel tells Clark that the true test of a hero is that he might have to kill one to save many. Clark says that even if it is your own son? He tells Lionel that Lex was abducted this morning at the field. Lionel goes to the field and Lex is back. Lionel and Lex talk about Lex has made a deal with the devil and he always comes to collect. Lionel grabs Lex by the shoulder and Lex throws him 100 yards away. Lex now has super powers. Lex runs off back to the mansion.
Lana is there and she is glad to see Lex. Lex tells Lana that he is okay and that he has been given a gift. He pulls out a gun and shoots his hand to demonstrate, he catches the bullet. Lana is amazed that he isn’t scratched. Lex tells her that she needs to tell the truth about him. He has their abilities but he isn’t one of them. Lex tells her that he couldn’t keep something like this from the person he cares about the most. Lana then tells him that she overheard Clark and Chloe talking and that Clark is going to try and kill him. Lex believes that it is his father’s fault for infecting him with fear. Lex tells her that he has to go somewhere, Lana wants to go, but he tells her no. Lex tells Lana to meet her at the top of LuthorCorp Plaza tonight.
Lionel is at the hospital and Clark comes in and Lionel tells Clark that he found Lex and that he has changed. Lex now has powers like him and that he is dangerous. Lionel believes that Lex was chosen by Zod because of the darkness in him. Lionel warns Clark that Lana is in danger too.
On the LuthorCorp plane, Martha and Lois board and find a bottle of wine and a card from Lionel. Martha states that she isn’t interested in a relationship with Lionel. Lois doesn’t believe her.
At the Luthor mansion, Clark comes looking for Lex. Lana is there and they talk about how Lex is in trouble. Lana doesn’t believe him and won’t tell him. Lana asks Clark to tell him what is happening to Lex, Clark doesn’t answer and Lana tells Clark that she can’t believe she ever loved him and then walks out. Fine appears behind Clark and tells him that if he would have told her the truth about him, then Clark would have her allegiance. Clark then punches Fine, and Fine tells Clark that he was supposed to be the vessel and release Zod the first time. Clark tells him that he will never release Zod. Fine tells him that he will use Clark’s weakness of caring for humans to manipulate him. He then uses a computer program to shut down all the power.
At The Planet, Clark finds Chloe and they talk about how the computer virus is shutting everything down. Havoc and panic are occurring throughout Metropolis. All of a sudden, a car comes through the window and Clark saves Chloe. They talk about how now the only option is to kill the vessel of Zod. Clark goes to leave, and Chloe says that she doesn’t know if she will ever see him again. Chloe gives him a passionate kiss. Just then a phone rings and Clark answers it. It is Lex, who says that he heard Clark was looking for him.
On the LuthorCorp jet, Martha and Lois start talking about how it sure is taking them awhile to get to Washington. They look out the window and see they are not anywhere near the East Coast, as there are snow covered mountains below them.
Clark goes back to the Kent farm and is in the barn when Lex walks in. Lex asks Clark if has decided to kill him. Clark tells him that Lex did this to himself. Lex confronts Clark how he used to think that Clark was so virtuous, but realizes that Clark lies to everyone he cares about. Lex tries to throw Clark, but Clark throws him. They fight and Clark pulls out the knife to kill Lex, but can’t do it. Fine appears and encourages Clark to kill Lex. Clark instead kills Fine with the knife. A red beam shoots out from The Fortress and Zod is released into Lex’s body. Zod’s confronts Clark and tells him Lex is dead. Zod tells Clark that Jor-El banished him to an eternal hell and that the only survivor is Kal-El. Clark tells him that it is between them and no one else. Zod tells Clark that he needs to join him and Clark says that he will never join him. Zod then is able to imprison him in the Phantom Zone.
In the LuthorCorp jet, Lois and Martha are running out of oxygen. Martha passes out and Lois is able to pry open the oxygen masks, but passes out before she can put them on.
News clips from all around the US are shown of people rioting and looting. In Metropolis, Chloe is stuck in the middle of a riot. Lionel shows up in his limo and Chloe gets in, but they are pulled out and assaulted. Lana is also in the middle of Metropolis heading for the top of LuthorCorp. She manages to arrive and finds Lex there. Lana tells Lex that she is there for him and wants to find out where this will take there relationship. They kiss and the camera pans to Metropolis and then the US and then the world and how it is in chaos. Tjhe camera pans to space and we see Clark trapped in the Phantom Zone flying away from Earth.