In the middle of the night on the road, a young pregnant woman is going into labor while the father of her child drives, when she suddenly glows and implodes, while the guy stops the car and runs for his life. Lana and Clark are driving a truck along the same road and find a baby in the crater created by the explosion. They take the baby to the hospital, and the Kent family temporarily guards him, who is connected to Clark. Lana and Clark give the name of Evan, and on the next day, he becomes a teenager, precociously aging. The scientists of Lex study the case and conclude that the boy needs a transfusion of the bone marrow of his unknown father, if he can be found, and even then... Clark tries to save Evan. Meanwhile, Genevieve Teague has a meeting with Lionel Luthor and threatens to hurt Lex, in case the missing stone from China is not delivered to her. But Lionel soon turns the tables on Genevieve by poisoning her (the same way he unsuccessfully tried to poison Lex in the previous season) and threatens not to give her the antidote unless she gives him the second missing stone whom she in fact stole from the murdered Bridget Crosby.

With Clark banished to the Phantom Zone, Metropolis is in shambles as the city riots, and Chloe & Lionel plot to rid Lex of General Zod...one way or another.

Clark is thrilled when he learns that his friend, Raya, managed to escape from the Phantom Zone and has come to see him in Smallville. The two grow close and Raya shows Clark how to restore power to the Fortress of Solitude. However, Baern, the spirit of a killer with the ability to control and feed off electricity, also has escaped from the Phantom Zone. After possessing the body of a street kid in Oakland, California, Baern makes his way to Smallville to take revenge on both Raya and Clark for his imprisonment. Meanwhile, Lana gathers more information about Lex's research project called ROCK. Also, Jimmy Olson returns to try to win back Chloe's affections by tailing Lana to find any dirt on Lex Luthor.