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In Smallville and the comics, Jonathon dies both times by a heart attack and also dies directly or indirectly from Brainiac. As Brainiac was the antagonist in season 5, he indirectly with manipulating Clark many times caused his heart to get worse of the stress and anger. In conclusion, Brainiac not only destroyed Clark's homeworld but also indirectly and directly caused the death of Clark's adoptive father. Brainiac is a cold, cunning, computer that has no remorse and no possible redemption for destroying worlds. For that I think its another piece of proof that he is the worst villain against Clark. Jonathon's stress over losing martha, dealing with his distrust of brainiac, and realizing he almost killed clark can put a lot of stress on a heart and could've indirectly made him die.