Clark and classmate Eric Summer are both struck by lightning while Eric is holding a meteor rock, and Clark's powers are transferred to Eric. While Clark experiences normal humanity, the emotionally challenged Eric goes on a rampage.

After stealing an experimental flower laced with meteor-rock pollen from Dr. Steven Hamilton, the employee of the Luthor Corp, James Beales has a truck accident on the road and is rescued by Jonathan Kent. However, the flower releases its pollen on Jonathan's face, and he unleashes his innermost repressed desires first with Martha and his anger towards the Luthors. He enters in coma later. Then Lana becomes affected and tries to seduce Clark. Pete also becomes affected by the Nicodemus flower in the same way. While Clark helps Lex track down the source, Lex hides from Clark that Dr. Steven Hamilton is working for him, but they find the cure in an old book.

Clark saves Lana from the tornado, leading Lana to be suspicious of Clark. While protecting Clark's secret, Jonathan gets trapped with reporter Roger Nixon in an underground mausoleum. Lex and Clark search for Jonathan.

When Lana is assaulted by three drunken customers at The Talon, Clark defends her and ends up throwing the main antagonist onto the new Sheriff's car. The new uptight Smallville sheriff, Nancy Adams, arrests Clark for assault and battery but later dismisses the charges and gives Clark 40 hours of community service instead. Andrew Connors, the man that Clark threw onto the Sheriff's car, fakes a serious injury and attempts to sue the Kents. With the abrasive Sheriff Adams unwilling to help Clark and his family, Lana decides to help Clark expose Connors as a phony. Meanwhile, Helen is stalked by her ex-boyfriend, Paul Hayden. When Paul attacks and nearly kills Helen, a vengeful Lex teams up with Clark to track down Paul to the train station before he can skip town.

When Jonathan goes to Smallville Medical Centre for a physical examination, his doctor diagnoses arterial blockage and recommends a triple bypass heart surgery procedure. Meanwhile, Vince Davis, the older brother of Clark Kent's friend Garrett Davis, needs a liver transplant - but does not receive one and he dies. His body is sent to Metropolis to be the next test subject of Lionel's experiment by Dr. Lia Teng, who injects his dead body with experimental blood platelets and revives him. When Vince gets sick again (because he needs the life-sustaining blood injections on a daily basis), the unstable Garrett loses control and becomes a threat to the patients, employees, and visitors of the hospital by showing up at the hospital with a kryptonite-infused bomb strapped to himself, threatening to blow himself up unless his brother receives a new liver transplant. Clark must try to find a way to defuse the situation during Jonathan's heart surgery, while the overzealous Sheriff Adams wants to kill Garrett in any way possible... even at the expense of the hostages. Meanwhile, Chloe does some investigating for Lex of Dr. Teng and learns about the mysterious blood platelet serum she's manufacturing and about the first test subject: Adam.

Clark is thrilled when he learns that his friend, Raya, managed to escape from the Phantom Zone and has come to see him in Smallville. The two grow close and Raya shows Clark how to restore power to the Fortress of Solitude. However, Baern, the spirit of a killer with the ability to control and feed off electricity, also has escaped from the Phantom Zone. After possessing the body of a street kid in Oakland, California, Baern makes his way to Smallville to take revenge on both Raya and Clark for his imprisonment. Meanwhile, Lana gathers more information about Lex's research project called ROCK. Also, Jimmy Olson returns to try to win back Chloe's affections by tailing Lana to find any dirt on Lex Luthor.