Anyway, now there were 52 universes, which were all copies of New Earth, except The Fourth World and Earth-C, which were counted among the 52. Also, everyone remembered the old multiverse and their histories in it, but also remembered their current histories on New Earth, so everyone just had two sets of memories. At least people who existed Pre-Crisis. But anyway, a year later, Captain Marvel villain Mr. Mind, a superintelligent venusian worm, revealed that he had used Booster Gold's time traveling robot sidekick Skeets as a cocoon, and absorbed chronal enegeries while morphing into his adult form, which now was a giant multiversal moth that existed outside the multiverse and ate pieces of the universes until the heroes stopped him, but in the process he changed all those copies of New Earth so they were now different, and they mostly happened to be fairly similar to some of the more important Pre-Crisis universes. But when Power Girl, a survivor of Earth-Two who never fit into New Earth properly, went to the new Earth-2 (note "-Two" vs "-2"), she found that it was very similar, but not actually the same universe she left. It was just a copy.
Also, Earth-Three? The backwards universe? That was where The Crime Syndicate lived. The evil Justice League. They died fighting the Anti-Monitor, but DC decided they were too good a concept to waste, so they had a new Crime Syndicate which was now explained to be from Qward, the anti-matter universe, which always existed and didn't have its reality altered by the Crisis. So I guess if Earth-Three was never destroyed, there would be two Crime Syndicates.
Well two Crime Syndicates is nothing, because now there was also Earth-3, with a third Crime Syndicate. But the Qwardian Crime Syndicate kept appearing and was basically more important, with the Earth-3 Crime Syndicate kind of being a footnote... for now.
So Final Crisis happened, but unlike Crisis on Infinite Earths and Infinite Crisis, it doesn't really change the multiverse much. But they do clarify that now on the 52 Earths there are 52 Monitors, one watching over each Earth. Oh yeah, also the Anti-Matter universe is also called Earth-(-1) now so I guess there are technically 53. The main Earth, once known as Earth-One, and later New Earth, was now known as Earth-0. And the Anti-Monitor was brought back to life by Green Lantern villain Sinestro, but he was never as big a threat. Anyway Final Crisis is confusing as fuck, but in two tie in issues which are actually the most important part of the story, Superman Beyond, which has nothing to do with Batman Beyond, Superman goes to The Monitor Realm and finds out that the original two Monitors (including the Anti-Monitor) from the Crisis on Infinite Earths aren't even the same kinds of beings as these Monitors, who perhaps more clearly could be called Over-Monitors. They're actually just probes sent by one of them to experiment with the Multiverse, but when he did so, he was corrupted by the Multiverse, since now he was technically a part of it, and he became addicted to feeding off its energies. Because see the Over-Monitors are metaphors for the editors and publishers meddling with the stories. Which means they see things from a semi-meta perspective. So they know the whole history of the multiverse like we do, but also they're sort of part of it, so their perspective isn't quite as high as ours. Or maybe it's higher, because don't forget that Earth-Prime is part of the multiverse, so maybe the Over-Monitors are beyond even us.
Anyway, Superboy-Prime has still been messing around trying to "fix" the multiverse, and eventually the heroes just send him back to Earth-Prime, where he becomes a shitposter on the internet. Because oh yeah, Earth-Prime, the real world which was destroyed by the Anti-Monitor, has now been recreated by accident by Mr. Mind. Of course, it's not literally the same world, but both are still treated as our world. I guess technically the second one must be our world, since the first was destroyed. This means that our world didn't really exist before 2007, and everything you think you remember before then is actually just reality being warped by a superintelligent venusian worm from another universe that grew bigger than the multiverse and ate parts of our reality.
In 2011, The Flash went back in time to save his mother from being killed when he was a child, which didn't used to happen anyway, but Reverse Flash went back in time and killed her. But for some reason it was Flash's fault when this broke time, and a character named Pandora had to merge three timelines together to stabilize the timestream. One of the timelines was the "Vertigo" timeline, which really was just the DCU anyway, so we can figure this timeline was exactly the same as the main DCU timeline, so that probably helped things not change so much. But there were still changes.
Among these changes, now the Justice League only formed five years ago, and Superman became a superhero about a year before that. Now, in Post-Crisis continuity, Superman appeared ten years before the Crisis on Infinite Earths, so this was a big change. Everyone was a lot younger. But keep in mind that all the major events were still canon, except for ones that were explicitly contradicted. The Crisis on Infinite Earths, Zero Hour, Infinite Crisis, and Final Crisis all still happened, but now all in five years. And it's not like those were the only multiversal threats, just the only ones that were both multiversal threats and also changed the fabric of the multiverse.
Other changes included things like Wally West, the third Flash, being erased and replaced with a young black kid whose story was just starting. The Justice Society was also seemingly erased. But don't worry, because the Justice Society on Earth-2 still existed. But of course, they weren't really the original Justice Society. And now they really weren't, because the timestream changing affects the entire multiverse, so now they were super different than before. They weren't old, for one thing. But that was really the least of it.
Also, Earth-3 was changed, but it still had a Crime Syndicate, and this Crime Syndicate was much more important than the Pre-Flashpoint Earth-3 Crime Syndicate. Nobody really talked about the Qwardian Crime Syndicate anymore, even though they technically should still exist.
Oh yeah, also, just like in the Crisis on Infinite Earths, the Legion of Superheroes continued unchanged, even though that was just ridiculous. And I think at one point they claimed that actually now the Legion was actually on Earth-2, but that's just even more fucking ridiculous. Idk, I never got really into this Legion. They still showed them interacting with Superman when he was a kid.