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.