Originally Posted by
BlitheringToot
Beast should join the Avengers proper, and Storm and Iceman should join the Uncanny Avengers, with Storm leading the team.
With them gone, Nightcrawler becomes headmaster of the JGS. The school faces a massive threat in the form of Bishop's new Brotherhood of Evil Mutants, made up of other future X-villains such as Raze, Xavier Jr., and another time-displaced Trevor Fitzroy; lesser-known Claremont villains like Tartarus of the Neo and the unused second Super Sabre and Commando from X-Men #106; Unus, Siena Blaze and Astra. This Brotherhood's motivation is shaping the future of mutantkind--since Bishop and the future Brotherhood members from "Battle of the Atom" are trapped in this time, they figure they might as well make the best of things rather than attempt to go home again, and the JGS stands in the way of their plans. When all looks bleak, Cyclops and the New Xavier School arrive and helps fend the new Brotherhood off. With Beast and Iceman out of the picture, the JGS is now pretty much devoid of crazies, and Nightcrawler extends a hand of friendship to Cyclops, who accepts it, and they hash out the new status quo of the X-Men.
First, Cyclops concedes that it's kinda fitting for the school to be named after Jean, no matter how crappy Wolverine's intentions might have been at the time, and the school keeps its name. Cyclops and Nightcrawler agree that in some respects Logan was right--most young mutants have no interest in "the cause" and just want to learn to live a normal life. That being the case, the school itself is designated as a "safe zone." The Danger Room is still in effect so students can practice their powers, and they still learn basic self-defense, but the militarization aspect is toned down. The JGS remains a relatively fun and lighthearted place. Goldballs, Hijack and company are very happy to have nice beds to sleep in again instead of cots in the Weapon X facility.
However, on the edge of the property an underground bunker has been built. This is where Cyclops, Magik and crew train, and it's where the students with dangerous powers (or merely dangerous minds) go to hone their combat skills. It's not a hellish "Full Metal Jacket" environment or anything, but Scott makes it clear: this bunker is the school's chief line of defense. This is the War Room. This is where $#!+ goes down. And the final exam for mutants taught there is a fight with Danger.
So that's the basic scenario: Nightcrawler running the school, Cyclops as field leader, Bishop as the big bad. Eventually Scott and Emma would get back together, because let's face it, they're an awesome mutant power couple, and I reeeeeally want Ruby Summers to actually happen.
The public perception of the X-Men would change as well. Nightcrawler would be active promoting the school in media, and he's so darned likable it actually works. Attendance booms for the first time since Decimation, and nobody's stupid enough to try blowing up another school bus becaaaaause the likes of Cyclops and Magik are intimidating enough to keep anti-mutant harassment low. Cyclops' crew gets more involved in superheroics and is hailed as heroes after a few good team-ups, but even though they're not hated anymore ... they're definitely feared. Which is exactly how Scott wants it. So basically on one side you've got the grinning, gregarious Nightcrawler making you comfortable with the idea of mutants, and then on the other side you've got Cyclops and crew reminding you why they shouldn't be messed with. A good balance, I think.
There would also be yet another new X-Force, this one led by Maverick with characters like Mystique, Gambit, Forge, Marrow and Psylocke onboard, along with Tartarus' estranged sister Elysia. They wouldn't be as "black ops" as the past few incarnations, but they'd still know how to get their hands dirty. Fantomex will not be in this one.