The only times I can distinctly remember him interacting with Lois or Clark directly happened in Season 3. In Season three, he is the one who it preparing Lois to move into a new body during the Arrrrrcgh! I don't ever remember Clark interacting with him. I thought he had during "I've got you Under my Skin" but when I read the script I realized all the Asabi/"Clark" interaction was actually someone else in Clark's body.
CLARK: No. I'm just worried I'm a jinx. JONATHAN: A jinx? CLARK: Yeah. Let's face it, ever since she's known me, Lois's been kidnapped, frozen, pushed off buildings, almost stabbed, poisoned, buried alive and who knows what else, and it's all because of me. -"Contact" (You're not her jinx, you're her blessing.)
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