In 2002, long before Lost when Abrams was best known as the creator of Alias and Felicity, he turned in a revamp script titled Superman: Flyby that got Warner Bros. super excited. In this script, Abrams proposed nothing less than a complete reworking of the entire Superman mythology. New origin. New backstory. New powers. New relationships. How new? Well, Krypton doesn't explode, for starters.
Instead, Krypton is engulfed in a Civil War between King Jor-El and his evil brother. The evil brother seizes power, but fails to stop Jor-El from shooting his infant son (you-know-who) to safety in a spaceship. Apparently, it's important for the bad guys to kill Baby Superman because he's (get ready to roll your eyes) "The Chosen One" of an Ancient Kryptonian Prophecy; so they dispatch thousands of their own spaceships to track him down.
In this new continuity, the Kents have been covertly pre-selected by Jor-El to foster parent Superman a la Mary and Joseph, but instead of being innately heroic, the new Clark Kent grows up an introverted emo kid afraid of his own powers - which now mostly include being super-strong. He needs to be wearing the Superman suit, which is now a Venom-like living-costume with a mind of its own, to fly.
Lex Luthor is a CIA agent in charge of UFO hunting, who's walking around pissed at his superiors about a Dark Secret. When the evil Kryptonian army invades Earth to take down The Chosen One, Luthor teams up with them to kill Superman. No, really. Superman dies!
... and goes to Heaven, where he gets a pep talk from his dead father about The Prophecy that helps him come back to life, rise from the grave and lead humanity in a rebellion against the Kryptonian invaders. Oh, and in a final setup-for-the-sequel stinger: After all the Kryptonians are defeated, Lex Luthor shows up to challenge Superman to a fight (it'll make sense in a moment) and reveal that Dark Secret of his ... he's from Krypton, too!