An experiment at the Luthor fertilizer plant makes an old friend of the Kents literally shake and jitter, and he seeks vengeance against the Luthors, who hide the secret of his transformation behind "Level Three" at the local plant.

After an explosion Lana finds herself getting visions of a serial killer...and his next target is Chloe. Meanwhile Lex and Roger look further into the meteor shower and determine that something besides meteors hit Smallville that day.

Lex is hit with a surprise after his father closes the local Smallville plant to force him back to Metropolis, blaming the plant's failure on his management. Meanwhile Clark prepares for his date with Chloe, reporter Roger Nixon gets wind of Clark's alien origins after setting up an explosion, and Whitney joins the Marine Corps. Lex works with the workers to buy the plant and put it under local management, and his father Lionel threatens to sabotage the efforts by buying up their mortgages. It all comes together when Nixon uses the "key" Lex found (in "Obscura") to activate the spaceship just as three tornados hit Smallville. He flees into the storm with Jonathan in pursuit and Martha left to confront the opening spaceship. The tornado hits Lex's manor and traps Lionel under beam, leaving Lex with a life-or-death decision to make. And Clark arrives to see Lana whisked up into the tornado. (to be continued...)

A Smallville student, Ian, displays the ability to make clones of himself and uses his power to date both Chloe and Lana. Meanwhile Lex goes to anger management class and meets an attractive local doctor.

Kara, a beautiful superpowered girl from Krypton, entices Clark to join with his father and embrace his destiny. Clark is left without support after Pete's departure when Jonathan reveals the deal he made with Jor-El. At the same time, Clark's relationships with Lex and Lana take unexpected turns, leaving him with no one but Kara to turn to.

After discovering that Chloe's body isn't in her coffin, Clark and Lois Lane investigate but are stopped by Lois' father, General Sam Lane. They believe General Lane knows more then he's telling, and figure out he's been in contact with Lex. Meanwhile, after Lana's sudden departure Jason follows her to Smallville. And Lionel sends a mutant killer to determine if Chloe is alive and kill her for sure.