Clark has some weird dreams with the cave and about flying. When he puts the octagonal key in a hole in the wall of the cave, he immediately learns how to decode the symbols. Then, while waiting for Chloe at the Kents' farm, his uncontrolled vision burns a symbol on the wall of the barn. Chloe publishes the picture in the front page of The Torch, and Clark soon receives an e-mail from a wealthy and prominent scientist from New York. Clark goes to New York and meets the reclusive and quadriplegic Dr. Virgil Swann, who tells Clark about his origins from the planet Krypton, his real birth name of Kal-El. Clark also finds another message in the spaceship which troubles Clark. Elsewhere, Dr. Waldon finds the octagonal key left behind in the cave and when he puts it in the cave hole, he gets hit with the so-called Kryptonian knowledge which overloads his brain and ends up in coma, which further fuels Lex's suspicions about the cave and Clark. Also, Lana considers moving out of Chloe's house to look for a place of her own.

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.

The Kryoptonian metallic disc is returned to Clark following the death of Virgil Swann. Placing the disc in the cave reveals a message from the spirit of Jor-El instructing Clark to find the three Kryptonian knowledge crystals and unite them before others find them and use them to self-interest. The message goes on to tell Clark that allowing a human to assemble the crystals could lead to the destruction of Earth. The first stone, retrieved by Lex in Egypt in the season opener, is in Clark's possession in the cave. The second is apparently in possession of the late Swann's associates. And the third is located somewhere in China. Clark joins forces with Lana where they venture to China to search for the stone where Lex and Jason are also on the hunt for the stone. But they end up captured by the Chinese authorities and tortured for information to the stone's location, and it leads to the spirit of Isobel once again commandeering Lana's body to fight everyone to take the stone for herself.

The story of Clark Kent culminates in this two-hour series finale as Clark takes the last step to becoming the Man of Steel.