A deranged policeman who survived the attack of the Kryptonians and his policewoman fiancée break into Lex's mansion asking for the location of the spaceship so they can go public with the news of "aliens on Earth". But Lex locks himself in the panic room. Clark accidentally finds the association of Lana with Lex in their research of the spacecraft when Lana is kidnapped by the renegade cops to force Luthor to leave the room. Lex gets shot, but Lana escapes to the panic room with him. Meanwhile, Jonathan presses Lois to find out who is funding his campaign and Martha tells the truth about Lionel.

Clark reveals his secret to Lana, Jonathan and Lex learn the results of the senatorial election, and there is a tragic car accident on the highway that takes the life of someone Clark loves, forcing Clark to appeal to Jor-El for help.

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.

Clark, Oliver, Lois and Dinah are back home after long VRA captivity, with confused memories and robbed of all superhero-powers. They believe they have been tortured in an experimental lab by none other than Chloe, hence fear she switched sides. Then she, or rather her avatar, appears in dreams to each of them, claiming they only lost their powers in a virtual illusion, which can nevertheless kill them for real. She calls upon them to trust her, break the virtual spell by believing it fake and thus escape back into reality, with Rick Flag's team. Oliver does so quickly, and is reunited with his true love. Clark wants to, but finds it extremely hard, until Lois joins in.