While on the roof of the barn, Jonathan is contacted though the octagonal key and Clark saves him from a fall. Clark goes to the Kawatche caves with the key trying to find an explanation for what happened, when Lionel Luthor unexpectedly appears and expresses his suspicion towards Clark. Lionel goes to New York and secretly meets with Dr. Virgil Swann and proposes an association to investigate Clark. Meanwhile, the FBI is revealed to have bugs in Lex's mansion for a surveillance to obtain evidence against Lionel, and Clark becomes a suspect due to the interest of Lionel in the apparently simple "farm boy". Later, agents, led by Frank Loder, arrive at the Kent farm to search it for the missing octagonal key, leading Clark to mistakenly believe that Dr. Swann betrayed him to Lionel. Meanwhile, Lana cannot seem to make up her mind whether she wants to stay with Clark or not.

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.