- "This is your destiny, son. You are going to touch the lives of so many people. Not just as a man, but as a symbol. You're a symbol of peace. You're a symbol of justice." – Jonathan, to Clark, Void
Jonathan managed to survive the second meteor shower with minor injuries, but Martha was more seriously hurt. Lois Lane arrived to help Jonathan get Martha to the hospital. When Martha and Jonathan returned home, Clark announced that Jor-El had stripped him of his powers. Jonathan and Martha were shocked, but Clark maintained that he was glad to see them go. Shortly afterward, Jonathan, Martha and Lana were taken hostage by three metahuman fugitives who forced Clark to infiltrate a LuthorCorp facility and steal a serum to which they had become addicted. With Chloe's help, Clark was able to save the day without his powers.
When Jonathan and Martha found out that Clark and Lana had begun a sexual relationship, he gave Clark a stern lecture on responsibility. However, the subject was forgotten when, that same day, Clark was shot by Gabriel Duncan. Clark died at the hospital, but was resurrected by Jor-El who was using Lionel as a vessel. With his powers restored, Clark saved the entire town again and Jonathan told him that he was very proud. Jonathan asked if Jor-El wanted anything in return, but Clark denied this. Jonathan seemed skeptical, but he was, no doubt, so glad to see Clark alive again that he did not press the issue.
Jonathan's oldest friend, Kansas State Senator Jack Jennings, came to visit the farm in the fall to ask Jonathan to drum up support for his campaign. However, it was soon disclosed that Jennings had been having an affair with a stripper, Melissa Paige, who turned up dead. Jennings maintained that he had nothing to do with her death, but he admitted to the affair. Jonathan took him to task for failing in his duty to be a moral role model and Jennings decided that the scandal was too detrimental to his campaign and chose to drop out to work on his personal problems. He suggested that Jonathan run in his place. Jonathan was skeptical at first: Martha objected because she was afraid it would put unwanted attention on their family, but Clark was unwilling to be the cause of Jonathan's reluctance.
While deciding to run, Jonathan was approached by Lionel, who offered financial support against Lex, claiming that it would be dangerous for Lex to win his first foray into politics. However, Clark had become infected with silver kryptonite and hallucinated that Jonathan was planning to turn him over as a test subject in exchange for Lionel's money. In a rage, he assaulted Jonathan and Martha before he was subdued by Chloe. Jonathan and Martha learned that Chloe had learned Clark's secret a year ago. When Clark was restored to normal, he urged his father to make his decision on what he thought was best and to not let fear of his secret being exposed ruin their family's life.
Clark's deal with Jor-El was revealed when Martha contracted a strange Kryptonian illness. Clark admitted that Jor-El predicted that his life-force would be exchanged for one of his loved ones. Worried about Martha's deteriorating condition, Jonathan was angry that Clark had not told him and instructed him to handle the situation. However, the illness was caused by Professor Milton Fine: Clark defeated him and Martha was cured. Jonathan approached Clark again and in softer tones, advised him not to dwell on Jor-El's warning and live life to the fullest.
Jonathan's campaign was in full swing by Christmas of 2005. He hired Lois Lane as his campaign manager and she and Martha managed his finances. However, Martha was approached by Lionel, who again offered to finance Jonathan's campaign. Not wanting him to lose simply because they were out of money, Martha accepted his offer. When Jonathan found out, he blamed Lois, but later had to apologize when Martha admitted responsibility. Jonathan decided to mortgage a sizable portion of the farm, known as the "Back Forty," to pay Lionel back. When Samantha Drake, a deranged fan of Lex, began stalking Jonathan, she and her henchmen beat him up and tied him from the rafters of the barn. He was not seriously injured, so Samantha hatched a new plan to force Lois to shoot Jonathan during a speech. However, Clark and Lois were able to stop Samantha, and Jonathan was saved. It was revealed, though, that the stress the campaign was beginning to affect Jonathan, and he began to have heart trouble again. The attack bolstered Jonathan's popularity even more, and on January 26, 2006, Jonathan defeated Lex in the election and won the race. They held an election party at the Talon in his honor. While the producers never revealed which party Jonathan Kent belonged to, he was a staunch advocate of farm subsidies.
Unfortunately, this night, Jor-El's prediction came true. The night of the election, Jonathan received a phone call asking for a meeting at the barn, and he left the party to meet the caller. Newly engaged to Clark, Lana was killed in a car accident. Clark was devastated, and Jonathan drove by the scene and stopped to comfort him. Clark begged Jor-El to reverse time so he could prevent Lana's death.
In the altered turn of events, Jonathan met the caller: Lionel. Lionel asked for a partnership in his term, and showed Jonathan a photograph of Clark emerging unscathed from an explosion. Jonathan reacted with anger and declared that the Luthors would not ruin his family. He beat Lionel up in a rage, and told him to stay away from them. Martha and Clark arrived home to find Jonathan staggering out of the barn. He collapsed into his family's arms, and died that night.
The entire town of Smallville attended Jonathan's funeral, including both Luthors. Clark confessed to Martha that he blamed himself, but she tried to assure him that there was nothing he could do.