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- "As much as I loved my father, I... a part of me still resents him for needing me that much. I don't want you to feel that. That's not the kind of father I... I ever wanted to be." – Jonathan, to Clark, Forever
Jonathan was comatose for three months in the Smallville Medical Center, during which time Clark's whereabouts were unknown. He miraculously and suddenly awakened when Clark returned reprogrammed as Kal-El and Martha used black kryptonite to restore him as Clark. However, Jonathan's heart problems continued and he was prescribed a variety of medications to combat them.
The football issue again caused conflict in Jonathan and Clark's relationship when Clark joined the team again against Jonathan's wishes. Clark insisted that he was much older and able to control his powers, but Jonathan again thought Clark would hurt another player. However, Clark stood his ground and Jonathan allowed him to stay on the team.
Jonathan was almost run down in Metropolis by a sleepy driver, but his life was saved by Bart Allen, a young man who could run faster than Clark. When Clark and Lionel switched bodies, Jonathan didn't seem concerned by Clark's strange behavior (unlike Martha), but he was injured when Lionel-in-Clark threw him across the kitchen.
During one of Clark's football games, Clark was controlled into tripping by Mikhail Mxyzptlk and caused one boy to suffer a minor injury. Jonathan told Clark to quit, but Clark was firm in his belief that the injury was not his fault. He told Jonathan that he makes a conscious decision to react normally with every physical contact and that there was no way Jonathan could ever understand. Jonathan conceded and Clark went on to take the football team to a state championship.
Jonathan and Martha were part of several victims of an airborne toxin that caused several Smallville residents to hallucinate their worse fear. Clark found them passed out and was able to help Lex create an antidote and save them. Shortly afterward, Clark reunited with Alicia Baker, as well as Martha and Jonathan once again told Clark that they disapproved of their relationship. However, under the influence of red kryptonite, Clark ran away with Alicia and "married" her in Las Vegas. Although the marriage wasn't legal, Jonathan was so angry with Clark for his lapse in judgment that he wouldn't even face him. When Alicia died, Jonathan and Martha were uncharacteristically smug and didn't offer Clark any useful coping advice.
Clark received a football scholarship from his parents' alma mater Metropolis University. However, when he met Met U football player Geoff Johns, who admitted that he had been forced to start using his powers in college due to the added pressure of the game, Clark decided that he would not be able to play college football and conceal his powers and turned down his scholarship.
Jonathan was bitten in the arm by a kryptonite-enhanced Rottweiler, but saved by another dog, a golden retriever. Clark learned that they were products of a failed LuthorCorp experiment and Jonathan warned him that they would most likely be destroyed. Clark pleaded with Jonathan to let him keep the golden retriever. Jonathan relented and Martha named him "Shelby."
Jonathan and Martha chaperoned Clark's senior prom, even though Clark didn't want to go. Jonathan's presence proved invaluable when the spirit of would-be Prom Queen Dawn Stiles possessed Chloe. As Dawn, Chloe pushed Jonathan down the stairs, but he was revived by Clark. When Dawn's spirit leapt into Clark, Jonathan forced her out with green kryptonite and restored Clark to normal.
As Clark's high school graduation approached, he revealed to his parents that he had turned down his Met U scholarship to attend a closer college. Jonathan and Clark both knew that he would be unable to run the farm without Clark, but Jonathan urged Clark to make his decision based on what he wanted, not what was best for the farm. He admitted to Clark that he resented his own father for needing him and didn't want Clark to feel the same way. However, Clark displayed the maturity and sound reasoning his parents instilled in him, insisting that he wanted to stay and help with the farm.
On the day of Clark's graduation, they received word of another impending meteor shower and Jonathan and Martha were forced to evacuate. Clark revealed that he had to stay behind because he had neglected to fulfill Jor-El's task of reuniting the Stones of Power. Jonathan and Martha reluctantly prepared to leave without him, but they were taken hostage by Jason Teague, who threatened to kill Martha unless Jonathan told him where Clark hid the Crystal of Knowledge. However, Jonathan managed to attack Jason by surprise, but a meteor hit the Kents' house.