The Beyonder's Multiverse ranges from Earth-40000-Earth-40099. It was created by an alternate version of the Beyonder, who grew bored with his reality. So he destroyed and recreated these 100 Earths in order to give himself unlimited entertainment. Each Earth is unique and different from each other in almost every way. Beyonder enjoys tampering with each Earth, but often sits back and enjoys the show.
In Earth-40000, Peter Parker was never bitten by a radioactive spider. But when his Uncle Ben was shot, he went into a coma. Peter became desperate for help, so he made a deal with the devil, Mephisto, who turned Peter into the Ghost Rider in exchange for Ben's life. When Ben recovered, he and May were disgusted in what Peter had become, so he ran away in order to eradicate crime, regular or hellish, as the Ghost Rider. His most formidable foe is the Spider-Demon.
Reed Richards' space flight was funded by S.H.I.E.L.D., so after he and his crew crash landed the Fantastic 4 became Agents of S.H.I.E.L.D. Mr. Fantastic, Invisible Woman, Human Torch, and the Thing instantly become some of the world's most popular heroes. They spend most of their time fighting the eco-terrorist and director of HYDRA, Victor von Doom. During one battle, Doom murdered Sue, causing Johnny to resign from S.H.I.E.L.D., but Reed and Ben remained partners in S.H.I.E.L.D.
After coming to Earth, the Venom symbiote was not discovered by Spider-Man. It was discovered and taken by the Fantastic Four, but it managed to take control of Mr. Fantastic, Invisible Woman, and Thing. Human Torch's powers kept him safe, so he left to get help. Johnny joined the Avengers, and the rest of the FF were arrested because the bond had become permanent and the three of them now had linked minds.
This reality is very similar to Earth-616 in many ways, but very different in others. Spider-Man was willing to kill when it was necessary, causing New York's crime rate to decrease. This eventually caused Spider-Man to cross paths with the assassin/mercenary known as Deadpool. The two became best friends and later partners. They now fight crime together under the radar, killing any criminal they can.
In this reality, Loki formed the Masters of Evil, consisting of Baron Zemo, Abomination, Leader, Enchantress, Executioner, M.O.D.O.K., Crimson Dynamo, Living Laser, Grey Gargoyle, Magneto, and Taskmaster. The Masters wiped out all heroes, but kept Captain America, Iron Man, and the rest of the Avengers as trophies. The new heroes of the future, Doom, Spider-Man, Majorpower, Mechagoblin, and their leader, Wolverine.