- "Look, Clark, I'm your father. I'm supposed to have all the answers. It kills me that I don't, but you gotta have faith that we'll figure this thing out together." – Jonathan, to Clark
When Clark was 14, he began to question his strange abilities. After emerging unharmed from being hit by Lex Luthor's car, Clark stuck his arm into a running wood-chipper in front of his shocked father and demanded answers: Jonathan had no other choice but to reveal the truth. He showed Clark the spaceship in the storm cellar and explained how Clark fell from the stars, but emphasized that it didn't matter to him or Martha.
When Clark decided to join the football team, Jonathan was concerned that Clark would hurt other players, but Clark insisted that he had his super-strength under control. Jonathan's point was proven when Clark made a super-powered leap over another player during practice. Fortunately, they reconciled when Clark quit the football team.
When Sam Phelan infiltrated the Kent's life to gain information about Clark, he framed Jonathan by placing a body in the barn and manipulated Clark into stealing for him in order to release his father. However, Clark was able to conceal his secret and turn Phelan in and the charges against Jonathan were dropped.
The Kent Farm was plagued with long-standing financial difficulties, but Jonathan refused to accept Lex's advice or financial help, saying he did not want to owe the Luthors anything ever again. He encountered Bob Rickman, who could control people's will with a handshake, and found himself inexplicably selling the farm, but was able to get the contract voided.
Jonathan was infected by the Nicodemus flower and displayed strange and erratic behavior. Normally reserved, he openly made out with Martha in the kitchen and when he learned that his loan had been rejected, he took a shotgun to the bank in a rage. Clark was able to stop Jonathan from entering the bank with a shotgun but, to his shock, Jonathan shot Clark in the chest just before he collapsed. Clark enlisted the investigative skills of his friend Chloe Sullivan and was able to find a cure.
Throughout Clark's freshman year, Jonathan and Clark frequently disagreed on Clark's budding friendship with Lex. Jonathan believed Lex to be a self-serving, destructive young man, as well as indirectly indicated that he did not think Lex was the best influence on Clark. Despite Lex's repeated displays of kindness and thoughtfulness, Jonathan was short with Lex and sometimes even openly rude. He was furious when Dominic Sanatori informed him that Lex had been investigating the Kents since Clark saved his life and he and Clark had an argument about the friendship yet again. Clark seemed determined to show Jonathan that Lex was not like Lionel and always defended him. For his part, Lex idealized Jonathan and Clark's relationship, seeing it as something he could never have with his own father. He did not like being a cause of strife in their relationship and always encouraged Clark to work things out with Jonathan.
As a high-school freshman, Clark developed new powers, strengthened his existing ones, as well as received the unwanted attention of Roger Nixon, an investigative reporter hired by Lex. After confirming Clark's invulnerability, Nixon finally confronted Jonathan about his unusual son the same day several tornadoes hit Smallville. When Nixon threatened to expose Clark's abilities, Jonathan exited the safety of the storm cellar to track Nixon down.