He goes back in time and becomes Leo Quintum. Superman knows that–but nobody else ever figures it out, because, like Clark Kent, Quintum is always wearing glasses.
Here’s a bunch of corroborating evidence from the series:
Chapter 1, pg. 7: “Lex Luthor told the world he had reformed and for some reason the whole world believed him.” Reforming Lex Luthor is an impossible task–the idea is unthinkable. But maybe that’s Superman’s ultimate victory: the secret labor that no one can ever know.
Chapter 1, pg. 8: The first time we see Luthor himself in the series, as he’s sending his voice into the mutated creature that’s yelling at Leo Quintum. And here’s what General Lane is saying in that panel: “Lex? Are you talking to yourself again?” (More on Techland: All Star Superman To Become Movie, With TV Star Cast)
Chapter 1, pg. 15: Quintum explains to the sun-poisoned Superman that “Luthor has used us to kill you.” Then, on the next page, he gives us his raison d’etre: “I’m trying to escape from a doomed world too, Superman… it’s called the past.” His past, anyway.
Chapter 1, pg. 17: Quintum tells Superman that “I promise we’ll find a way to save you. Or to replace you, if we have to.” Not quite as potent a promise as it sounds at first.
Chapter 3, pg. 13: “a condition of quantum uncertainty, neither alive nor dead.” Perhaps Quintum exists in a state of quantum uncertainty too, since it’s never made explicit whether he’s Leo or Lex.
Chapter 4, pg. 22: Leo Quintum’s wardrobe is “365 rainbow coats, all identical!” Luthor always did like to wear the same oufit. But note that the rainbow coats are Luthor’s colors (green, purple, orange) plus Superman’s colors (red, yellow, blue).
Chapter 5, header page: Luthor’s prisoner number is 221. 2+2+1 = 5, as in “quint.” Lex is also the fifth person named on page 1.
Chapter 5, pg. 20: Note that Luthor’s Superman-baboon is named Leopold.
Chapter 5, pg. 22: “If it wasn’t for Superman, I’d be in charge on this planet!” Lex says. Quintum, naturally, has access to infinite assets.
Chapter 8, pg. 7: Quintum explains that “it was Lex Luthor’s intention from the start to kill Superman using the sun itself.” And he’d certainly know what Lex’s intentions were.
Chapter 10, pg. 15: Superman believes in everyone… even Lex. “I know there’s good in you.” (More on Techland: Up, Up and Away: 10 Non-Superman Supermen)
Chapter 10, pp. 18-19: “I could be the devil himself for all you know,” Quintum tells Superman–but Superman hands over his genetic information, saying “this is how much I trust you, Leo.” (We know that he can read people’s genetic codes and identify them by their heartbeats; if Leo is Lex, he can tell. But All-Star Superman involves a lot of people pretending for convenience’s sake that they don’t know each other’s secrets–it’s pretty clear from Chapter 12 that Jimmy knows Clark is Superman.)
Chapter 11, pg. 8: Luthor throws Nasty a hat that strongly resembles Leo’s sidekick Agatha’s hairstyle.
Chapter 12, pg. 2: “Doctor Lex-Or.” In old Superman comics, Lexor was the name of the planet where Lex was a hero and Superman was reviled as a villain.
Chapter 12, pg. 16: “You could have saved the world years ago if it mattered to you, Luthor.” And he may yet save it years ago.
Chapter 12, pg. 21: Lex, Quintum says, “seems so faded, so small, now that he finally got his dearest wish”–now that Superman has literally become all-star.
(Credit where it’s due: I picked up most of these observations from things written about All Star Superman by Cole Moore Odell, Marc Singer, David Uzumeri, Joe McCulloch and Neil Shyminsky.)
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