A tornado buries Jonathan alive along with reporter Roger Nixon who has uncovered Clark's secret. Nixon has video of Clark's spaceship, which was activated with the missing "key" and flew from the cellar as the storm began.

What's up with Lana? Clark rescues Lana from the twister. She suffered a mild concussion, and thinks she saw Clark's face as she was trapped in the truck, whirling in the twister. Lana can't understand how she survived, and suspects Clark is keeping a secret.

What's up with Clark? Clark is frantic, searching for his dad. Clark avoids Lana's probing questions about her rescue, telling her he found her after the tornado.

What's up with Jonathan? Jonathan chases reporter Roger Nixon into the storm. After the twister, they are trapped in the underground crypt of an old church, with a trailer crushed above them. Jonathan has the chance to kill the reporter, but instead helps him from the rubble. Nixon challenges Jonathan with words about Clark. Jonathan demands the videotape from Nixon for a way out, he surrenders it, Jonathan destroys it. As they try to escape, they are buried in more rubble.

What's up with Martha? Martha remains strong, despite the disappearance of Jonathan. She even comforts Lana, sharing the story of her memory from the day of the meteor shower (from season 1 Pilot). Lana, a child playing make-believe, asked Martha to make a wish and Lana granted it with her magic wand. Martha wished for a child. "Soon after, Clark came into our lives," Martha tells Lana, confiding she's glad Lana and Clark are close.

What's up with Lex? Lex offers to help in the search for Jonathan. Lex confides in Clark that he hesitated saving his father Lionel when he was trapped. Lionel is in critical condition at the hospital. His doctors disagree on surgery. One wants to operate immediately. The other feels its too risky, and suggests waiting until Lionel is stable. Lex decides to have them operate immediately.

What's up with Lionel? Lionel survives the surgery, and will walk again. He thanks Lex for saving his life during the twister. Then he tells Lex he should not have allowed the immediate surgery, although Lionel would've decided the same if Lex had been injured. The surgery has left Lionel blind, and he tells Lex he should've let him die.

What's up with Chloe? Clark apologizes to Chloe for leaving her at the dance, and wants to make it up to her. Lana has already told Chloe that it was Clark who found her. Chloe tells Clark she just wants to be friends. Clark accepts this, and walks away. Pete finds Chloe crying.

How it ends: Clark finds Jonathan and Nixon, but cannot help them because he is weakened by kryptonite rocks scattered at the site. Jonathan tells Nixon of the kryptonite and its effect on Clark. Nixon stuffs a kryptonite rock in Clark's jacket, and pulls him outside. Jonathan runs out after Nixon. They struggle, and Nixon strikes Jonathan, threatening to kill him. Lex arrives and shoots Nixon dead. Jonathan thanks Lex for saving his life. They shake hands "to a fresh start."

Later Clark tells his dad "I felt like I was flying...as if I willed it..." when describing Lana's rescue.

We see the spaceship in the middle of a field, where it landed during the twister when the "key" was dislodged.