Pete finds Clark's spaceship, forcing Clark to reveal his secret to his best friend. Dr. Hamilton is plagued by kryptonite-fueled illness and focuses on Pete. Meanwhile, Lana has to deal with Nell and her plans to remarry while Lex and Lionel adjust to life together.

A strange woman shows up claiming to be Clark's biological mother...and that his father is Lionel. Meanwhile Lana decides to meet with the man who is her biological father.

Clark becomes involved with a Native American woman, Kyla, and becomes aware of ancient Indian prophecy that warns of a man of great powers who fell from the sky. Worse, a wolflike creature is attacking the local Lexcorp construction project, and Martha and Lionel may be the next victims.

Lex hires some thugs to bug Lionel's office but things get out of control when Lionel and Martha are taken hostage, and Clark must rescue them without revealing his secrets.

Lex recovers his long-lost brother Lucas and uses him in a ploy to buy out his father's share of the company. But it soon becomes clear that Lucas isn't to be trusted, and Lex soon finds himself ousted from his own company.

After a schoolmate claims to be an alien and proves it by using heat vision, Clark investigates and believes the boy is from Krypton. Meanwhile, Helen confronts Lex over the locked room in the mansion that holds his investigation of Clark's secrets.

Lana is haunted by the ghost of a dead friend, Emily, but the "spirit" has connections to Lionel Luthor, who is also scheming to get control of the Indian caves and "help" Lex with his wedding.