Superman Returns

At around the same time that the movie Superman Returns came to theaters, Superman returned in the comics in a somewhat similar story.

Superman #653

Up, Up, and Away part 7

Lex Luthor attacks Metropolis with the Kryptonian crystal warship he unearthed, and which he claims belonged to Dru-Zod.  General Zod had previously appeared in different alternate version in the post-Crisis era, but this was his first mention in this new era where the real General Zod would finally exist again in a few years.  The images of a belligerent, spacefaring Krypton are a departure from the sterile, isolated planet that was characteristic of John Byrne's reboot.

Superman questions why Luthor didn't take advantage of the year without him to actually do some good for humanity, like Luthor always claimed he could have without the Kryptonian.  With some help from Jimmy Olsen, Superman defeats Luthor, hurtling himself into the Kryptonite crystals and extracting Luthor from the ship.  Both Superman and Luthor hurtle uncontrollable through the sky, and as they begin to fall into the bay, Luthor tells Superman how he hates him.

Action Comics #840

Up, Up, and Away part 8

Luthor and Superman both survive the fall into the bay and wash up on shore.  Superman is still weakened from the Kryptonite, so Luthor sees this as his opportunity to fight on equal ground.  But of course, Superman easily knocks him out by page 5.  

The Man of Steel spends the rest of the issue getting back to normal, both as Superman and Clark Kent.   Jimmy Olsen meets with Superman in private and gives him the sunstone crystal that he found after the fight with Luthor.  Superman uses the cyrstal to make a new Arctic Fortress of Solitude, and the status quo resets back to normal.  Virtually all the changes to the status quo prior to Infinite Crisis have been undone now.

There still wasn't a definitive post-Infinite Crisis origin story.  Fans were in the dark as to what precisely had changed in Superman's past, although it was evident there had been a major retcon.  In next month's Justice League of America #0, for instance, readers would see Clark Kent sealing up the secret tunnel he used to enter and depart the Kent farm as Superboy, something that hadn't been seen or referenced in over 20 years.