And so, Nick Fury recreated the multiverse, but fixing several things that he did not like. First of all, he honored his deal with Mephisto and recreated Hell, but in a way that he would be confined to it and could never reach the realm of the living, not even through dreams. They never discussed the specifics. Even devils should beware when bargaining with Nick Fury of SHIELD. Then, his home universe. The Gah Lak Tus swarm, for example, was an aberration that served no good purpose, so he erased it. It never existed. The Kree and Skrull (including the Chitauri) remained, but never developed faster-than-light speed and stayed confined to their own solar systems. The Norse gods only visited Earth during the Viking Age, and never returned. As for human history, however, he preferred to leave most of it untouched. Evil still exists, war still exists. He understood that there's always a delicate balance between causes and consequences and that a small change could have unforeseen ramifications. For example, he could easily prevent WWII from happening. Or better, both World Wars. But if the Holocaust never took place, if it didn't exist as a paramount example for all countries of the extremes they did not want to reach, then the Universal Declaration of Human Rights and the many movements that requested social rights for minorities in the later decades may not exist either. The state of Israel may not be formed either and Jews may still be a community without a country to call home. So he swallowed the hard pill and kept it.
There was, however, a change he did make for the world at large, starting with WWII: the super-soldier program. He made a big change to the universe: superpowers would not exist. He also granted Steve Rogers a better body; not much, just the basic for him so that he was not rejected. He proved to be a war hero regardless, in a WWII without aliens or supersoldiers. He even survived the war and returned home, to get married to his beloved Gail. And like falling dominoes, the absence of a super-soldier program prevented everything else. Weapon X never created mutants: Charles Xavier, Erik Lensherr, Scott Summers, Logan, and others never got any special powers. Oscorp never tried to recreate it with the Oz serum, which means no Spider-Man, no Green Goblin, no Doctor Octopus. And with nobody to try to recreate a serum that never existed, Bruce Banner never became the Hulk, and Betty Ross never became She-Hulk.
The lack of superpowers did not make the world a utopia, anyway. The United States and the Soviet Union started an arms race anyway, even if for the development of conventional weapons. Or not so conventional: atomic bombs had the power to destroy the world just as easily as Magneto or the Maker on a rampage would. But they were never fired, cooler heads prevailed, and after a few decades, the Soviet Union could not keep up with the pace and collapsed under its disastrous economic policies. The world was shocked again when a group of terrorists stole a plane and crashed it at the World Trade Center, which started the War Against Terror.
Of course, many of those who were superheroes would still meet anyway, and many things still happened in similar ways, even if with no superpowers involved. Ben Parker was killed by a thief, but Peter and his friends from school made the detective work themselves and helped the police to bring the criminal to justice, and kept doing so later on. Superpowers or not, nobody tells Peter Parker to stay on the sidelines when someone needs help. He graduated with honors and started a software firm with another promising talent from another school, Miles Morales.
Charles Xavier still made his school, but not as a facade for a superhuman group. It was really a school for gifted people. Scott Summers, Jean Grey, Ororo Munroe, Henry McCoy, Piotr Rasputin, and others all met in it and became great friends. But not Logan. He was from the WWII era and loved his cigars. With no healing power to stop his aging or to counter the effects of tobacco, he died of lung cancer before the school was created. And not Alison Blaire, who stayed with her band. Dazzler was a huge success, kickstarting a new wave of American Punk Rock.
Tony Stark also started making weapons for SHIELD but changed his mind when the doctors discovered that tumor in his brain. But instead of making a combat armor, he joined forces with Steve Jobs and they took the digital revolution to even greater lengths. They have invented several devices for communication, work and entertainment, and made them cheap and accessible for all publics. In a few years, people could not conceive life without their awesome devices.
Reed Richards and Susan Storm also met in the Baxter Building, another school for gifted youngsters. They made several inventions, even if Reed felt at times a bit constrained by the requirements to keep his inventions focused on what he was ordered to develop. They worked on the space projects for the exploration of Mars, and eventually, Reed Richards, Susan Storm, Jonathan Storm, and Benjamin Grimm, the "Fantastic Four" as they came to be known, were the first humans ever to set foot on the Red Planet. They even found life in it, just a few cells, but enough to start a scientific revolution. Returning as worldwide celebrities, they had now full funding and freedom to develop anything they wanted. And from then on, only the sky was their limit.
And with his universe restored and improved, Fury continued with the restoration of the other ones. Now it was the turn of the universe that clashed with his during that incursion...