- "No, I didn't shoot Lionel. But I let my anger get the best of me. I... I haven't exactly kept it a secret how Jonathan Kent feels about the Luthors. What jury could possibly believe me now?" – Jonathan, to Martha, Suspect
During the tornadoes, Jonathan exited the storm cellar against Martha's protests to go track Nixon down and prevent him from exposing Clark's powers. They were trapped underneath a building for almost a full day. While trapped, Jonathan received harsh criticism from Nixon, who said that Clark was a world wonder, not his farmhand. Jonathan stood his ground, maintaining that Clark was merely the son he raised. When they were rescued by Clark, Nixon incapacitated Clark with green kryptonite and tried to kidnap him and Jonathan fought Nixon brutally. However, the matter resolved itself when Nixon was shot by Lex just as Nixon was about to deliver Jonathan a fatal blow.
When Clark suddenly developed heat vision, Jonathan was able to reassure him that he was not a danger to others by helping him learn to control it. He was also influenced by the pheromones of Desirée Atkins and almost killed Lex, but Clark was able to stop him.
Clark defied his parents and told his best friend Pete Ross his secret. Jonathan and Martha were angry at first, but decided that Pete could be trusted after all. Pete's help proved invaluable when he had to help Jonathan subdue Clark when he became volatile and reckless under the influence of red kryptonite.
When Jonathan's father-in-law, William Clark, came to visit, Clark asked Jonathan to explain why they didn't get along and Jonathan was forced to reveal his and William's shaky past. In addition, when Rachel Dunleavy came to town claiming to be Clark's mother, Jonathan was also forced to reveal his role in helping Lionel Luthor gain influence in Smallville.
Martha gained the opportunity to be Lionel's personal assistant after he was blinded during the tornado storm and the job caused friction in her relationship with Jonathan. When Jonathan broke his leg trying to repair the tractor, Martha felt extreme guilt for not being there to help and offered to quit. Jonathan told her his concerns that the Luthors come first, but knowing that she really enjoyed her job, told her not to quit if she didn't want to. However, when she and Lionel were kidnapped and held hostage in LuthorCorp, Martha learned that Lionel was investigating Clark and decided to quit. Surprisingly, Jonathan recommended she stay, in order to be close to Lionel and see what he knew.
Jonathan's issues with Lionel came to a head when he was framed for shooting him by the sheriff of Smallville, his old friend Ethan Miller. Jonathan's name was cleared, but he regretted vocalizing his distaste for the Luthors so publicly.
Jonathan's perception of Lex improved when Lex was kicked out of the Luthor Mansion and sought refuge at the Kent Farm. Jonathan gave Lex strenuous and unpleasant farm chores, but Lex pulled his own weight. He admitted that he was surprised and pleased at Lex's work ethic, telling him that he would have made a fine farmer. Jonathan and Lex parted on good terms, but Jonathan was injured again by Lucas Luthor, who cold-cocked him with a gun.
Jonathan faced the reality of losing his family when Martha and Clark were infected with kryptonite spores and became deathly ill. The seriousness of the situation was heightened when Jonathan learned that Martha was pregnant. Determined not to lose his family, he broke into the Disease Control Agency warehouse to reclaim the key to activate Clark's ship and cure both Clark and Martha. The Kents prepared for their new arrival with hope and excitement.
Shortly afterward, Clark was contacted by Dr. Virgil Swann and learned more about his alien heritage than ever before. Jonathan supported Clark when he opened the ship for the first time and they read a message from Clark's birth father together. Clark began to panic and got upset when he realized that his biological father intended for him to conquer Earth, but Jonathan assured him that he was not bound to any fate and could choose his own destiny.
As he prepared to marry Helen Bryce, Lex asked Jonathan and Martha to sit at the table with him and Helen at the wedding. Jonathan gave Lex a compass as a gift- a Kent family tradition, with the compass making sure that the groom didn't lose his way when he was walking up the aisle-, and told him that he thought he was turning into a fine young man.
When Clark encountered his Kryptonian father Jor-El for the first time, he was informed that the time had come for him to fulfill his destiny. Clark resisted and devised a plan to destroy the ship. However, Jonathan and Martha were on the way home and the pulse from the exploding ship caused their truck to roll. Jonathan was uninjured, but Martha suffered a miscarriage. Extremely guilty and upset, Clark had to tell Jonathan that it was he who caused the explosion. Faced with the burden of his and Martha's grief, Jonathan never directly blamed Clark for the loss of the baby, but he angrily informed Clark that he should consider the consequences of his actions. Clark's own guilt, coupled with Jonathan's words, caused Clark to dose himself with red kryptonite and run away from home.