Three months later. Lois Lane, the second cousin of Chloe Sullivan, arrives in Smallville trying to find the missing Clark Kent to help her to find Chloe's murderer. After being struck by a mysterious ray, she loses control of her car, and finds Clark naked with amnesia in a cornfield. She brings him to Smallville Medical Center, where Martha is with Jonathan Kent, who has been in an irreversible coma. Martha brings Clark back to the farm, expecting him to retrieve his memory. However, Clark is completely dehumanized, having been taken over by his alter-ego Kal-El, whose mission is to find three Kryptonian crystals to assemble into one. Meanwhile in Paris, Lana Lang has an American boyfriend, a young man named Jason Teague, and is having a good time with him, until things take a turn when she gets hit with a mysterious spiritual force containing the spirit of a long-dead witch. Elsewhere, Lex is struggling to recover from being poisoned as he travels to bring an ancient object retrieved from an excavation in Egypt which Clark/Kal-El is also after and uses his flying abilities to steal the crystal... in midair. Also, Lois visits the imprisoned Lionel to talk with him about Chloe, while Martha has a meeting with an associate of Virgil Swan's, named Bridget Crosby, who gives her a new type of kryptonite to combat Clark/Kal-El.

Lionel Luthor, using one of the Kryptonian stones, attempts to swap bodies with Lex but inadvertently transfers bodies with Clark, leading to him learning a few secrets, including that of Clark's powers.