- "Not a day goes by, Clark, when I don't regret not being able to be right here for you. I would do anything, I would give anything to able to get a second chance to get it right. You got that second chance, son. You could be the greatest hero the world has ever known. " - Jonathan to Clark, Lazarus
Jonathan appeared on the farm, consoling Clark after his meeting with Jor-El. Jonathan told Clark that he would be a great hero but first he had to overcome the greatest trial he will ever face, saying Jor-El was right about a dark force that was coming. Clark asked him what this force was, but when he turned back, Jonathan was gone.
Upon returning from the future and taking the advice of Brainiac 5 into consideration, Clark, clad in his updated Blur costume, went to Jonathan's gravesite, where he admitted that he had been unable to let go of the past, and of him. Saying that he will always keep Smallville in his heart, Clark stated it was time for him to move on. Taking Jonathan's old watch, Clark buried it under the grass of Jonathan's grave and says a final "good-bye" to his father, promising to become the man his father brought him up to be.
When Martha came back to the farm for Clark and Lois' wedding, she saw an image of Jonathan's face in a picture of the two of them. She then argued with Clark about selling the farm and about Jonathan. Martha said that Jonathan was with them both and Clark could see him too if he allowed himself to. Clark explained that he had before. When Clark left, stating he had to get rid of the past to move on, Jonathan's ghost stood in the house, looking sad over his son's decision.
Clark, confused, visited Jonathan's grave again where Jonathan's spirit appeared to him like he had before. He tried to convince Clark not to leave the past behind and to let him and his mother be there for him. He later appeared at Clark and Lois' wedding to Clark, nodding at him as he walked down the aisle and then, unseen to anyone else, took a seat next to Martha to watch the wedding.
When the planet Apokolips was coming to Earth, Jonathan spoke to Clark in the loft about how this was his time and that he had to let Jor-El guide him from this point on because he was starting a new chapter in his life. Martha arrived and Jonathan and Martha comforted Clark, the Kents reunited as the end of the Earth loomed. Clark left to go face the threat while Jonathan and Martha watched him depart the farm.
After Clark defeated Darkseid, he went to the Fortress where Jonathan handed him the suit, telling him to always hold on to Smallville. He proudly gave his son the suit which Clark accepted and then took flight with the suit, accepting his destiny.