Basically. X-Man was battling the X-Men and Legion was also involved and it resulted in X-Man and Legion creating an Age of X-Man alternate reality where there are no humans. Hope Summers did something that turned everyone into mutants and created a utopia for all mutants but things like physical contact and romantic relationships are basically outlawed and all new mutants are created in a lab. X-Man basically controls the entire reality and is quick to mindwipe anyone that seems to be remembering things the way they should be or just has the X-Men toss them in prison if its a repeated occurrence for them. Bishop and Jean Grey for some reason were constantly getting together so he had Jean mind wiped again and tossed Bishop into jail. Apocalypse of all people has a team of his own X-Men that are all pro love and physical contact preaching against the X-Men. Nightcrawler is also the most popular X-Men of all now thanks to his successful acting career alongside Megan of Excalibur.
About 90% of the mutant population were swept into that reality. Main characters that weren't are Cyclops who only just came back to life at the time the final battle with X-Man was happening and was given a choice by teen Cable to either join the fight or save the life of someone from his past. He saved the person from his past. Eventually Wolverine shows up along with Blindfold and Multiple Man. Blindfold doesn't last long but Cyclops and Wolverine lead an assault on a government facility and rescue the current New Mutants team that were all bonded with Warlock but included Moonstar, Magik, Wolfsbane, and Xian. Before leaving they also discovered Havok who was being used to power the facility. Dark Beast also got worked into that somehow and they took him prisoner. Meanwhile Hope went full villain along with zombie Banshee and formed a new Mutant Liberation Front. Scott's team stopped them but not before Hope shot Cyclops in one of his eyes. Dark Beast saved his life but not the eye so now his powers are all screwy again. Woilfsbane then left the team and was promptly beaten to death by a group of humans while the X-Men were dealing with what appeared to be a new Brotherhood led by Magneto but was only Joseph. Juggernaut was part of the group but quickly turned on Joseph and joined the X-Men while Kwannon magically appeared and killed Joseph. She then joined the group also and joined Wolverine in hunting down the humans that killed Wolfsbane. And somewhere in all of that is Emma Frost who apparently erased any memory of her existence from everyone except for Juggernaut.
And Cyclops does have all the memories of teenage Scott as well including being a member of the Champions with Ms. Marvel who he briefly rejoins during War of the Realms.