- After the meteor shower, Smallville was a suffering, scared little town. Luthorcorp gaining interest in the town and opening a plant there gave way for jobs for many in town as well as hope that was desperately needed. But when meteor freaks-people who got infected by the meteor freaks left scattered across town-began to pop up and stir up trouble, the Mayor was put in a corner and forced to turn to Lionel Luthor for help. On that day, a secret deal was made: Lionel will help the Mayor keep the existence of the meteor freaks a secret in exchange for the Mayor looking out Lionel's interests such as turning a blind eye on any shady activities that may be going on at the plant or any shady dealings that Lionel may wish to bring to Smallville. When the series opens, the meteor freaks are being held as a urban myth and nothing more which the Mayor and the Sheriff's office have been working hard to keep that way.
- In the beginning of the series, Clark is 15 years old. He possesss superhuman strenght and speed but has no knowledge of his alien origins. The Kents have been keeping that a secret from him in fear of him spilling the beans to someone who may tell the government that will have no hesistance in capturing Clark and torturing him for information. So the story they told him about his origins instead was that he left on the side of the road since he has no memory of the alien pod and his crash landing in Smallville and that they found him and adopted him. They have no idea who his biological parents are, which is the truth.
- Clark is wearing glasses out of necessity because of an accident that happened to him during childhood which would have damaged the eyesight of any normal human so Clark has to wear the glasses to keep up the appearance that he is normal.
- Clark is best friends with Pete Ross, who's the quarterback of the high school football team and who's known about Clark's secret since they were kids.
- He also has a crush on the sharp-tongued, egocentric Lana Lang who's a cheerleader and the most popular girl in Smallville High because of her relation to her father, who's the Mayor of Smallville. Lana also has a boyfriend named Whitney, who's the head of the football team that Pete is a part of. Both Clark and Pete are jealous of Whitney for more or less the same reason: they are in love of Lana. But Pete doesn't act on his crush on Lana which he keeps to himself for the sake of his friendship with Clark.
- Lex Luthor is 18 years old and a low-level employee in his father's company. He's been trying to drown his sorrows in partying and casual flings with women but those haven't been enough to make him forget his meager role in Luthorcorp.
- In the series premiere, Clark begins his sophmore year of high school. An incident involving a meteor freak occurs at the Luthorcorp plant. Lionel needs to send someone to assess the situation and find out the cause of the incident. Lex steps up to the task to prove to his father that he has the potential to be more than just a low-level employee.
- During the course of his investigation, Lex meets Clark who gets curious about what happened in the plant and begins to look for the meteor freak responsible. A friendship blossoms between Lex and Clark when they join forces more or less to stop the meteor freak.
- By the end of the episode, Lex decides to stay in Smallville to run the plant and to continue his newfound friendship with Clark. Urged by a mysterious silent partner who tells him that there's someone in Smallville who's connected to the meteor freaker who may be the reason for Lex's desire to stay in Smallville, Lionel becomes very curious about Lex's decision and sends someone to keep an eye on him and anyone he comes in contact with.
- At the Kents' home, Clark learns about the secret his parents have been keeping from him for years. Since learning the secret, Clark has been feeling responsible for the meteor freaks and what was once an innocent curiosity about them turns into a duty to look after the meteor freaks and protect the people of Smallville from the dangerous elements among the freaks.
- Also in the series premiere, it is mentioned there has been a increase in meteor freak activities over the recent years and the reason for it has yet been discovered. And Mr. Kents learns from his doctor that there has more strain on his heart which requires him to start taking things easy if he doesn't want to have a heart attack in the future.
- Pete doesn't like or trust Lex Luthor, whose father took his family's farm away from them. He is jealous of Lex's friendship with Clark, who believes there is good in Lex despite what Pete has said about him. But Pete finds comfort in a fellow student named Alicia. Pete falls for her and learns that she is a closet meteor freak.
- Meanwhile, Clark becomes increasingly curious about the meteor freak activities and begins to believe they aren't random and that there is some kind of pattern to them like someone is causing them to attack the way they do. At some point, Clark comes across something that makes him suspect that Whitney may have something to do with the meteor freak attacks. So he decides to join the football team to get close to Whitney to slyly find out what he knows and what specifically he may hiding. Clark also uses his time in the football team to try out the sport that he’s always wanted to play since his father told him stories about his glory days at high school as a football team’s quarterback. Jonathan and Martha have issues with that along with Pete, who's afraid of Clark stealing the spotlight like he wasn't getting enough competition from Whitney in the football team.
- It turns out Whitney actually does harbor a secret. Years ago, his father got infected by one of the meteor rocks. At first, the mutation was small and Whitney’s father was able to hide it. But the mutation grew over time and it affected Whitney’s father’s ability to speak or move. Whitney kept his father’s condition a secret from the people of Smallville except a doctor in town who he brought in to check on his father’s condition when it became serious. When someone asks Whitney how’s his father, Whitney tells them that his father’s very sick and has to stay indoors. Whitney and the doctor run interference when someone tries to meet Whitney’s father personally or when questions concerning his father’s whereabouts become problematic. Whitney hasn’t shared this with Lana, afraid of what she may think of him, and so far has worked hard to maintain a normal life outside of home. But Whitney doesn’t know is that his father has the ability to influence meteor freaks with his mind and is responsible for the increase in meteor freak activities. At first, Whitney’s father was influencing the meteor freaks into attacking all things Luthorcorp-related in Smallville, possessing a burning hatred against the company and the belief that Luthorcorp has been making things worst in Smallville than better. When Clark got in the way of that and Whitney’s father learned about Clark and his abilities, he began to influence some of the freaks into attacking Clark to keep him from becoming a further obstacle in his personal war against Luthorcorp. He also saw Clark as trouble in Whitney’s relationship with Lana and what he wants the most out of his life is for his son to be happy with no one messing it up for him.
- Mid-season, Whitney's father uses one of the meteor freaks under his control to trigger Mr. Kent's heart attack to keep Clark off Whitney's back. Mr. Kent is rushed to the hospital and into surgery. Because of his father's situation, Clark puts his investigation into Whitney on hold and quits the football team.
- Late in the season, the Mayor finally stands up to Lionel by refusing to do any more offers for him and his company. Lionel warns him that he will regret this.
- Whitney’s father is defeated near the end of the season but his actions became the excuse Lionel needed to launch his plan against Smallville into action.
- . In the season finale, Lex’s father shuts down the plant and sends a government taskforce to Smallville to hunt down every meteor freak in town. Lex’s father is using the taskforce as a smoke screen to find Clark and bring him to a lab where he could find out what is special about him which attracts Lex’s attention so much.
- Whitney goes through a downward spiral after his father is ousted as a meteor freak but the events of the season finale prompts Whitney to stand up and be a hero to those being hunted down by the government.
- Lana is shocked when she witnesses Clark using his abilities.
- Lex saves the day by working out a deal with his father, who only listened to him because of some leverage Lex was able to gain over him. The deal is if he stops the chaos that’s going on in Smallville, lets the plant continue to run, and leave Clark alone, he’ll find out Clark’s secret for his father through their friendship and attempt to persuade him to join Luthorcorp as an invaluable resource. This way would be easier than forcing Clark to admit his secret and be subjected through experiments. But this will take time, Lex points out. Lionel agrees and puts forth the order to cease the hunt for any more meteor freaks.
- The meteor freaks already in custody are taken to a secret facility, feeling it would be unwise to release them to the public until they are sure they aren’t a threat anymore. Alicia is among the meteor freaks held in custody.
- The plant is re-opened and life goes on in Smallville like before…partially. People are still angry and shaken by the recent events. Lana keeps what she saw concerning Clark a secret but finds herself more curious about the man she used to barely acknowledge in the beginning.
- In the final scene of the season, Lex shares with Clark his deal with his father but assures him that he has no intention of bringing him over to his father. However, he will make the appearance that he’s doing his part of the deal because any sign that he isn’t would be an opportunity for Lionel to take matters into his own hands and use force to make Clark do what he wants. Touched by Lex’s act of friendship, Clark makes a profound decision to confess his secret to Lex. When the scene ends, we are left wondering how this will affect Clark’s friendship with Lex.