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.

At the Kent farm, Clark Kent is surprised in the middle of the night by a naked young woman claiming that she is Kara from Krypton, and asking him to go with her somewhere through the Kawatche caves to be "re-born" with the spirit of Jor-El. Kara also forces Jonathan to reveal the secret deal he made with Jor-El at the beginning of the season. Meanwhile, Clark decides to testify against Lionel to keep him in prison. Lionel sends a key of the secret chamber in the Luthor Mansion to Clark where he finally discovers the reason for the last three years of Lex's personal investigation of him, and he ends his friendship with Lex. Agent Loder continues investigating Clark's origins, until Kara finds him eavesdropping on the Kents and she eliminates Loder for good. Also, Lana leaves for Paris and Chloe and her father are included in the witness protection program. Events come full circle as Jonathan unsuccessfully tries to stop Clark from traveling through a dimensional gateway in the cave wall, Martha observes a Kryoptonia symbol that appears in a open field, Lex is alone in the mansion when he had a drink of brandy which is poisoned, Chloe and her father arrive at a FBI safe house... which explodes with them still inside, and Lionel accepts his new look in prison, but satisfied knowing that his revenge against all those involved with his incarceration has been accomplished.