"Vortex" is the thirteenth episode of the first season of Smallville and the 13th produced episode of the series. After Clark rescues Lana from the eye of the storm, he discovers the storm's wrath has unleashed the spaceship into the fields and buried his father alive.
The ship zooms straight for the tornado, presumably because that's where Clark is trying to rescue Lana. The key is dislodged from the ship by the tornado winds, and the ship deactivates and falls to the earth.
Clark makes his way to the truck Lana is driving. He climbs inside and holds her in his arms, protecting her from the flying debris all around them. The winds actually take the truck apart.
At the Luthor Mansion, Lionel Luthor is trapped under a column and has to call out to Lex several times before Lex helps him. When Lionel arrives at the hospital, he is suffering from multiple injuries, including "severe trauma to his optic nerve". He cannot be transported to Metropolis General, so specialists are being flown into Smallville. Lionel is well enough to give his son a hard time about hesitating before saving him. Lex apologizes.
Near the Kent Farm, Roger Nixon flees from Jonathan Kent with a videotape of the ship. He takes the tape out of the camera and puts it in his pocket. Jonathan finally catches up with him in an old churchyard cemetery where a mobile home falls on them and pushes them into an underground crypt. In the underground crypt, Jonathan finds Roger pinned under a monument and lifts it off of him.
The Smallville Medical Center is full of patients who have been injured by the tornado. Clark arrives with an unconscious Lana. When the doctor quickly confirm that she is going to be all right, Clark rushes off to check on his parents. He finds his mom in the storm cellar. She tells Clark that his father was outside when the storm hit. Clark rushes off to search for him. Chloe Sullivan finds Lana at the hospital. Lana tells her that she is sure Clark was there saving her, but it seems impossible. Chloe is glad to know what happened to Clark after the dance.
Lex arrives at the Kent Farm. He tells Clark about what happened with his father. He's worried that his father will ultimately interpret his help as a sign of weakness. Then they set off together to search the woods for Clark's dad. When they find Roger Nixon's car in a tree, Lex recognizes it, but tells Clark that he doesn't. Lex suggests that they might cover more ground if they split up.
In the underground tomb, Roger Nixon is searching for his cell phone, arguing with Jonathan Kent about revealing Clark's secret to the world. When the phone rings, it's Lex Luthor. When Jonathan realizes that Lex is involved in the conspiracy to expose Clark, he grabs Roger's phone and smashes it against the wall. Clark hears Lex talking with Roger, and he's so angry that Lex has lied to him that he storms off to continue searching on his own.
The next day, Martha tacks Jonathan's picture on the bulletin board of missing persons. The Red Cross has converted the Talon into a disaster relief center. Lana asks Clark how he found her, but they are interrupted. Martha tries to reassure Clark that this is not his fault.
Back in the underground crypt, Jonathan worries out loud about the lead in the foundation and tells Nixon that Clark can see through solid objects, but not lead. They continue to argue about the value and harm that revealing Clark's secret will cause. Jonathan has thought up a way out, but he won't reveal it to Roger until he hands over the videotape. He does, and they start to tunnel their way out where the mortar is weaker.
Lex goes to apologize to Clark. He tells Clark that Roger approached him last night, offering to sell him information about the Kent family, but Lex warned Roger to stay away from the Kents. He has brought a map that shows the location of the cell towers in the area. Since only one cell tower survived the tornado, they can narrow the search area to four square miles. Pete and Chloe join Clark in another search of the woods. While they search, Clark takes the opportunity to apologize to Chloe for leaving the formal. Chloe accepts the apology, but when Clark asks how he can make it up to her, she says that they really ought to go back to just being friends. Clark seems happy with her decision. However, she is obviously upset and begins to cry when she tells Pete what they decided. Pete just looks sympathetic. When they find the mobile home, Clark searches with his X-ray vision, but he doesn't see the crypt. Jonathan and Roger hear the kids' voices and start to dig faster, but it caves in on them. Jonathan is able to pull Roger from the falling debris, but they are both rendered unconscious, and the soil that has fallen into the crypt is full of Template:Meteor rocks.
At the Talon, Lana is watching a news report of her miraculous survival. Martha Kent reminiscences about how similar this disaster is to the meteor shower of 12 years ago. She tells Lana a story about that day. When Martha visited the flower shop, Lana was dressed as a fairy princess. She asked Martha to make a wish, and not long after that, the Kents adopted Clark.
Underground, Roger regains consciousness and realized that the cave in has cut off their air supply. Jonathan remains pinned under the debris, and tries to explain why they keep Clark's abilities a secret. He tells Roger the story of how when Clark was a toddler, he crawled under a 500-pound bed. Jonathan went to get him, and he just picked it up over his head. He and Martha decided to take him to a specialist who would be better equipped to deal with his abilities, but Martha realized that if they took him to anyone, they would want to keep him, so they decided to keep his abilities a secret.
Lex Luthor has to decide whether or not to let doctors operate on his father's optic nerve. One doctor believes that surgery must be performed as soon as possible; the other believes it should be postponed until his other injuries have healed. As a man of action, Lex decides to go ahead with the surgery immediately.
Pete has brought some old maps from the county planners office to the Kent Farm. He, Martha and Clark are going through them when Clark notices an old church near Hobson's Pond. It was destroyed during the Template:Meteor shower, but Martha speculates that Jonathan might have known about the crypt in the basement and sought refuge there. Clark rushes out to the site and lifts the mobile home off the entrance to the crypt. He enters the crypt and begins to pull his father from the debris when the meteor rocks overcome him. Jonathan explains to Roger that they make Clark sick and asks him to get Clark out of there. Roger takes one of the meteorites and puts it in Clark's pocket then drags him out of the crypt, saying that Clark himself will make better proof for his story than the lost videotape. When he gets him out of the crypt, he finds his car in the tree. Before he can make his next move, Jonathan tackles him. The two exchange blows until Roger gets his hands on a steel fence post. Just before he thrusts the post through Jonathan's heart, Lex Luthor shoots him in the back.
After being checked out by a paramedic, Jonathan compares notes with Clark. Roger told him that Lex paid him for information about the Kents. Clark says that Lex told him he wanted Roger away from the Kents. Jonathan concludes (incorrectly) that since the stories conflict, one of them must be lying. Clark points out that one of them just tried to kill him and one of them just saved his life. When Lex finishes giving his statement to Sheriff Ethan, he and Jonathan shake hands, determined to forge a new relationship.
Chloe is at the Template:Smallville Torch office. She is still upset about Clark, and considers deleting all of her photos of her and Clark at the dance together. Finally, she decides against it.
Lionel comes out of anesthesia after his surgery and tells Lex that there is every chance that he will regain the use of his legs, but the surgery to repair his optic nerve failed. He says he is blind and wishes he were dead. Lex is devastated by the news and he leaves the room without saying a word.
Clark talks with his father about saving Lana from the tornado. He says that he was propelling himself towards Lana in her truck and that it felt like he was flying. Lana finds Clark in his loft waiting for everything to get back to normal. She admits to Clark that she has always expected to die young, but Clark has saved her so many times, she is starting to think that there is more to him than it seems. He tries to brush her off, but Lana is unconvinced, and leaves, disappointed. He seems tempted to call her back and reveal Template:His secret, but he doesn't.
Meanwhile, the ship sits in a cornfield somewhere waiting to be discovered.
- "Oh, no! I won't say anything about your son, I swear to God! Please! Don't kill me!"
- "Clark is not a story. He's my son."
- (to Jonathan) "You have the most amazing being on earth doing chores on your farm!"
- (to Jonathan) "He's not your son, you deluded hick! He's not even human!"
- (to Jonathan after he destroys his cell phone) "You stupid son of a bitch!"
- "A tornado hit, people are in real trouble, and I'm upset because Clark didn't fulfill my fantasy."
- (to Martha) "You were like Supermom."
- "First time Clark used his abilities he'd crawl under a, a big oak bed that my grandfather had made. And I, I crawled underneath and tried to get him out. And then, all of a sudden, a frame just came up of the air. And he, he was a toddler and lifted a... I don't know, a what... 500 pounds over his head."
- "What did you do?"
- "We decided to take him to a doctor, scientist. Someone more equipped. Understand that we were... When got to the office Martha said that if we left him there... They would wanna keep him and we would never see him again. So I took him home. Now that may have been a mistake, but that was a mistake I'd gladly make again."
- "Time And Time Again" - Stretch Princess
- "In My Place" - Coldplay
- Whitney Fordman does not appear in this episode.