- "Clark, I've always told you to take responsibility for your own decisions. Now why don't you let me take responsibility for mine?" – Jonathan, to Clark, Legacy
Jonathan and Martha waited anxiously for Clark to return home after he ran away to Metropolis, even as the Kent Farm went into foreclosure and they prepared to move off of Jonathan's family's land. When Pete showed them evidence of Clark's escalating crimes, Jonathan resolved to force Clark to come home. However, Martha pointed out that Jonathan could not stop Clark or force him to do anything, so Jonathan went to the Kawatche Caves, where he established communication with Jor-El. They struck a fateful deal in which Jor-El temporarily bestowed Jonathan with Kryptonian powers.
Jonathan and Clark fought until he successfully convinced Clark to smash the red kryptonite ring and return home to face his problems. Lex also returned home and as thanks for accepting him into the family- as well as the compass Jonathan had given him, which had helped Lex make his way to the island where he had lived for the last few weeks-, he absolved the Kents of their debt and bought their farm in their name. Jonathan's terms of his deal with Jor-El were not immediately revealed, but the consequences of his temporary superpowers began to manifest as chronic cardiac problems: as a result, Jonathan's health began to decline.
When Clark was shot in the hand and shoulder with a kryptonite bullet by Van McNulty, Jonathan and Martha saved his life by digging it out with pliers and a knife. Jonathan also helped Clark adjust to a period of temporary blindness and helped him hone and control his newest ability, super-hearing. Jonathan was also one of several people affected by hypnotic e-mails and tried to kill Chloe, but she and Clark stopped him and broke the trance.
Jonathan suffered his first heart attack in early 2004 and had an extended stay in the Smallville Medical Center. Clark was convinced that Jonathan and Jor-El's deal was the reason for Jonathan's declining health and was extremely guilt-ridden, but Martha and Jonathan tried to assure him that it was not his fault. Jonathan later admitted to Clark that Jor-El's deal is probably why he had a heart attack, but he emphasized that he did not regret his decision. Jonathan was later recommended to have bypass surgery. He was initially reluctant to undergo the surgery, but Clark and Martha reiterated how important he was to their family. However, during the surgery, Garrett Davis took the entire hospital hostage in an attempt to save the life of his brother, Vince, even demanding that Jonathan's liver be given to Vince to save his life. Clark was able to subdue Garrett and Jonathan's surgery was a success.
When Clark heard a phone call from the future in which Lana Lang was being chased, he had Lana stay at the Kent Farm to keep her safe. Jonathan offered to watch over her while Clark and Chloe investigated the mysterious call. Jonathan let Chloe borrow his truck, but Lana's would-be attacker, Adam Knight, used it to track Lana down. He knocked Jonathan unconscious and abducted Lana, but Clark was able to save her.
In addition to his heart problems, Jonathan began to hear the beacon noise made by the key. He fell off the barn roof, but Clark was able to save him. Jonathan then began to display strange behavior and talked openly about how he regretted many of the choices he made in his life. He was drawn back to the Kawatche Caves where he and Lionel had an intense physical fight over the key before it flew into the cave wall and disappeared. Jonathan was seemingly returned to normal, but he could not explain what made him go to the caves and again did not tell Clark the circumstances of his deal with Jor-El. He continued to deal with his declining health problems, expressing to Martha that he was depressed and angry.
Jonathan saved Clark's life again when he was stabbed by Jeremiah Holdsclaw and almost bled to death. As he administered pressure to Clark's wound, his hands emitted a burst of energy and the wound instantly healed: Jor-El had used Jonathan as a vessel. Professor Joseph Willowbrook returned to tell Clark his theory that Clark was the fabled savior Naman and Clark talked to his father about the anxiety he felt over his destiny. Jonathan again assured him that he had the choice to make his own future.
Jonathan and Jor-El's deal was finally revealed at the end of Clark's junior year, when Jor-El attempted to convince Clark to accept his destiny by luring him into a pocket dimension with the reprogrammed Lindsey Harrison posing as a Kryptonian named Kara. "Kara" appeared at the farm and persuaded Clark to enter the dimension. She exposed the details of Jonathan and Jor-El's deal: That Jonathan would give Clark back to Jor-El when it was time for him to fulfill his destiny. Both Martha and Clark were extremely upset that Jonathan had made such a decision without telling them: Jonathan claimed he did not realize Jor-El would demand Clark back so soon. However, he had suspicions of "Kara"'s true motives and asked Chloe to run a trace on her fingerprints. When Chloe revealed that "Kara" was, in fact, Lindsey, Jonathan realized that Jor-El was deceiving Clark and went to the caves to confront him and stop Clark from entering. Jor-El began to strangle Jonathan to force Clark to return to him and Clark sacrificed himself to save his father's life. He disappeared into Jor-El's pocket dimension and Jonathan was left in a coma.