Originally Posted by
Harpsikord
Alright I've been sitting on this thread to actually think about what I think might happen.
First off, Scott and Jean choose to move through their problems, and as a result, Emma would leave the school just like she was going to at the beginning of Morrison's run (before going back to kill Cassandra Nova), and at the end of Here Comes Tomorrow. The school would be fixed and reopened with Jean and Scott as the co-headmasters, though Jean would be the one of the two more involved in the school aspect - they would lead the X-Men together and by council. Jean does not remain Phoenix, primarily because after her death at the hands of Magneto it is fractured and needs to piece itself back together. Cassandra Nova would target her in that first arc of Astonishing instead. M-Day would happen, no matter how much Jean might have tried to help Wanda with her post traumatic stress.
Unlike what happened under Emma as headmistress, the depowered kids first not be put on a bus and instead be flown home by the X-Men or given the option to stay with their friends and be given their education, and they wouldn't be killed by the Purifiers... at least not by missiles, because as soon as she became aware of them then Jean would have likely stopped them in place. The purifiers might have still tried to infiltrate the school, but it wouldn't have been as extreme or had the same effect. Messiah Complex would have happened, but differently; Jean would have been taken out of the event due to visions from the Phoenix like Rogue because of her coma. It's her idea to move to the west coast and a more secure location.
Second Coming would more or less happen the same way. Schism would happen, but not in the same way - it would still likely be Scott vs Logan, but I don't think Utopia would be as problematic as it was seen at that point. Jean would side with her husband because she largely doesn't disagree with the need to train these kids to defend themelves, and thinks that what Logan is doing is a half measure at best. AvX would happen largely the same, only - it's all a big fakeout. They think that the Phoenix is coming for Hope (though Jean isn't as convinced), but when it reaches the moon it merges with Jean, Tony blasts and kills her, and it splits into the Phoenix Five. The event largely continues the same way. When the Phoenix reconstitutes itself, it does so by reviving Jean, who (along with Wanda) uses Hope to bring mutants back.
Scott's revolution would largely be the same, only without Jean painting him as a straight up villain. If Scemma happens, it'd happen here, but I instead choose to view Jott as being like the Richards family - no matter what they go through they find each other again. Jean would, at this point, lead the X-Men at Xavier's - I think that she basically had the talk with the Phoenix at the end of AvX that she had at the close of Phoenix Resurrection, and is in a similar headspace here that she was at the beginning of Red. The X-Men being split probably does not last as long as it did in canon, the O5 never come forward to make Scott come to his senses because he isn't as extreme and because Jean is there. It's Jean that's on the Ark during Secret Wars. She's not stupid enough to try to fight Doom head on, so she probably survives the event to become one of the few who remembers what happened.
Now... Death of X and IvX. Scott and Jamie probably still die, but I don't think that Jean would have literally paraded around and done the thing. She would have informed the world of what the mists do, and when the Inhumans didn't respond, would have declared war or call to action because of Black Bolt's and Medusa's knowing inaction. Either way, IvX would happen sooner and not as extremely and the mists wouldn't get as bad as they did. Jean would still be leading the X-Men and they'd be in a better position through RessurXion (which would obviously not happen the same) and the events of Red would be the only thing to temporarily supplant her.
End of Grey's would still happen, and Rachel would be sent into space in place of Jean. Obviously Extermination and any story involving the O5 wouldn't happen the same, but maybe something like The Black Vortex still happened in some kind of way with the adult versions of the characters involved and maybe Battle of the Atom happened in some kind of way with Lil Xavier, Raze, and their Brotherhood.