Source: Superman: The Man of Steel Annual #3 (1994)
Type: ElseworldsWhat if the Kryptonians all came to Earth? (Take 2)
Based on: Action Comics #1 originally, but actually its retelling from Man of Steel #1
The true history: Scientist Jor-El tried to convince his fellow Kryptonians that their world was about to explode, but they didn't believe him. He only just managed to send his infant son on a rocket to Earth, where he would grow up to become... Superman.
Turning point: What if Krypton was doomed because of a plague?
Story type: New World Order
Watcher's mood: Frank Miller Lite narration
Altered history: In this Elseworld, the Kryptonians have contracted a plague, which made them flee to the only planet with the chemical composition necessary to arrest the deadly microbe and give them time to engineer a cure. Cold and unfeeling, they left their gestating chambers behind, except for Jor-El, who brought fetal Kal with him. He even managed to cure the child before it was born. The exodus was 23 years ago, and today, the Kryptonians hold sway over Earth. We're not exactly slaves, but we ARE servants, and the "cueballs" do have a code against killing. One man relentlessly fights them, and that man is a Bruce Wayne in his 50s, an aging Batman who is now more Kryptonian replacement parts than he has flesh and blood, and who plays a continual cat & mouse game with collaborator policeman Lex Luthor.
He's a little nuts. Shadowing him for some time now is Kal-El. The Kryptonians' only teenager, he was raised by the servile Ma and Pa Kent with good, wholesome human values, has let his hair grow out and is generally outraged by how his father's people treat humanity. Batman becomes an inspiration and when they finally meet, Bruce sees something in the kid. He gives him a suit based on the colors of the resistance movement and the name "Superman". And then he is seemingly killed by Luthor. To Jor-El's shame, Kal-El becomes a rebel against his own people, destroying many important installations and doing the inter-species diggity with resistance fighter Lois Lane.
She's a plant working for Luthor, but she really does fall in love with Superman (it's fate!) and helps him uncover what Batman was working on. She's the one who gives him the name "Clark" (it was her old brand of cigarettes) and together they visit Dick Grayson and Alfred and discover that Batman was going to attack an orchard where the Kryptonians were going to manufacture the cure for the plague. Without it, the cueballs were soon to die. Though his nannies, the Kents, try to talk him out of it, Kal plans to destroy the orchard and become the Last Son of Krypton. Lex has been waiting for his though, and he's gotten his hands on a chunk of kryptonite.
It's Lois Lane to the rescue. Kal is saved, but he also chooses another path. Instead of destroying his people, he tries to educate them (it was Lex's idea, really, even if it probably started as trash talk), siding with humanity and trying to reverse the tide. And hey, Batman turns up alive again. The World's Finest (the World's Only?) continue a "war that's just begun". First step was replacing Kryptonian flags with Terran ones, but I'm sure it gets more exciting after that.
Books canceled as a result: We really don't know what happened to Earth's other heroes, but we do know there would be Superman and Batman&Robin comics. Only ones you need, really.
These things happen: There's Take 1 of this What If?, of course. But in the real DCU? More and more Kryptonians have turned up alive, and some have tried to take over Earth. We're heading for a reboot on all that, but if I go by the Silver Age and the last couple years of Superman books, it looks like it's only ever a matter of time before the surviving population of Krypton balloons to rebootable levels.