The story of Superman has been retold many times in many media, with the basic facts rearranged. A common, but not universal, element is that sometime during his young adulthood, Superman endures the death of his adoptive father, the Midwestern farmer Jonathan Kent. (Somewhat less often, he also loses his adoptive mother, Martha.) As a consequence, Superman has the distinct tragedy of losing two sets of parents in a life which is otherwise generally gilded and overflowing with blessings.
Grant Morrison's twelve-part All Star Superman crafted a continuity all its own, largely drawn from continuities we'd seen before -- conspicuously the comics of the Bronze Age of 1972-1986. However, its depiction of the death of Jonathan Kent -- a heart attack suffered while he stood outside on his farm, leaving his wife Martha as a survivor -- more closely resembled the facts of Superman The Movie. This death, in issue #6, did not come as a surprise, as it was apparent on the cover of the issue. But there was a twist coming, a trick in which Superman even outwitted his younger self.
The issue unfolds with Clark Kent on a return visit to Smallville shortly after having moved to Metropolis. Mystery is afoot from the early going, with three strangers arriving to help with the Kent's harvest, with each of them looking like a figure from elsewhere in the All Star story or the Superman mythos. We soon find out that the three are future Supermen, apparently descendants of the original, on a mission to battle one of Morrison's great inventions, a lethal time-eating beast called the Chronovore.
As the three even-stranger visitors try to lasso the Chronovore, and keep the current Superman from getting entangled in the fight, the fatal moment draws nearer. Jonathan perhaps knows it's coming, telling the bandaged Superman, of Martha's plan to move into town, "It's the end of the line for me and the farm." Then he asks, clearly intuiting something of the nature of his farmhands, "He'll be okay, won't he? The boy." That last endearing appellation is perhaps owed to Eliot S. Maggin's Miracle Monday, in which Jonathan Kent calls his adopted son "the boy" as a matter of course.
When the Chronovore has prevented Superman from coming to Jonathan's aid, Superman realizes the loss, bitterly regretting the impotence of his mighty powers when it comes to the irreversibility of death. That's a regret expressed elsewhere in the comics and the movies when Jonathan's death comes about. But as he mourns, the twist (Superman had noted "There's something weird about all this!") is finally revealed to us when we find out that one of the future Superman is the original Superman, from the not-so-distant future, thankful for having had "the opportunity to see my Pa one last time." It's a moment that resonates brilliantly with his earlier mourning; Superman can't reverse death, but he can cheat it a little. At the end, it's hard to say whether Jonathan was more thankful to know that his boy would be all right or Superman to have truly said goodbye, and Superman has rarely felt so human.
At #4, is a sort of reverse angle shot -- we see a hero through a villain's eyes, and it confirms everything we ever thought about both of them.