John Byrne left Marvel in the earlier days of what is now called New Marvel, when Joe Quesada was made editor-in-chief. The cancellation of X-Men: Hidden Years was the cause. Ostensibly due to trying to focus the X-Men titles on a few books, Byrne says he was told many reasons. A phone call between Byrne and Quesada turned the air blue and that seemed to be that. Byrne won't work at Marvel until he receives an apology for the cancellation, Joe Quesada won't employ Byrne until he receives an apology for the phone call. And there it is.
But it doesn't mean that that Byrne has no more influence on the direction of Marvel comics. Indeed, it seems quite the opposite. Let's take a few important Marvel plotlines.
In House Of M, Wanda Maximoff creates an entirely new alternate reality, in which Magneto rules a mutant dominated world that has ground humanity into submission, including Marvel heroes. Wolverine recalls the real world however and gathers an underground troop to bring down the new system.
On West Coast Avengers, before his storyline was aborted by Jim Shooter, John Byrne had planned to use Immortus.
Discovering Wanda's power, he was going to kidnap her and use her to further his plans. And the first thing he was going to do was alter probabilities so that when the Avengers battled Kang the first time, Kang won!
My story would reveal this in flashback, however, as we would open in the world long after this had happened. Pretty grim place, where most of the familiar heroes had been killed off or never become super powered in the first place. No FF, since they never took that rocket ride. No Hulk, since Rick Jones has never driven his car onto the Gamma Bomb test site. (One of the main characters was going to be Peter Parker, who had not become Spider-Man because of Immortus' manipulations.)
As the story progressed, we would learn slowly what had happened — and also learn that we were not seeing "present day" Marvel, but rather a time a "few months" (Marvel Time) ago. The date would be just prior to when Thor, in order to save a wounded Black Knight, had used his hammer to open a portal in time and space and stuck the Knight into it. We would learn this when the Black Knight basically fell out of the air into the post-Kang's victory world. In that timeline, Thor had not placed him in the "time stasis", so when the changed world "caught up" to that moment, out popped the Black Knight. The multiverses intersected at that point, you see. Well, the Black Knight pretty quickly figures out what's going on, learns there is an underground (of course!) and helps the folk of the twisted version hunt down and stop Immortus, freeing Wanda (herself another link to the multiverse, by virtue of how Immortus has been manipulating her power) and setting everything right.
When all is restored, the Black Knight of course is back in that "hole in time", and Wanda is the only one who remembers how things were. A memory that fades, like a dream, very quickly. . .
One More Day is the Joe Quesada/JMS story in which Spider-Man does a deal with Mephisto, the devil of the Marvel Universe, which would erase his marriage to Mary Jane Watson as if it had never happened.
John Byrne and Howard Mackie created, but ultimately abandoned their own attempt to erase the marriage – and a lot more;
In a nutshell, Peter Parker's life goes completely to hell. Cut his life into the thinnest slices you can, and there will be something very, wrong with every slice. Everything has gone wrong.
He finds himself once more on top of the Brooklyn Bridge. This is the point where it all went to hell, he thinks. When Gwen died. Or when Captain Stacey died. Or when Uncle Ben died. Or when that damn spider bit him. There's no way to pick a point. It's all just blackness, blackness and more blackness. And…
He falls from the bridge. Did he slip? Did he jump? We'll never know. Because the last shot in that issue is him falling like a limp rag wrapped around a rock…
…And next issue he wakes up back in Queens, back in Aunt May's house, back in high school. Along with everybody else in his supporting cast, he's been rewound. Only, he doesn't know that. The readers know it, of course, but for Peter, it's business as usual — for maybe two issues. Then there's this little tickle at the back of his brain that tells him this isn't right. Look over there. Johnny Storm is twenty-something. Why does Peter think they should be contemporaries? It's just little things, but over the span of a few issues it brings him back to the Bridge again. Here. Something happened here. What? What happened?
"I happened," says the Shaper of Worlds, appearing alongside Peter. "I was drawn by your pain. I reached into your mind and found the last place you were happy. And I put you back there. I fixed everything."
"Well, UNfix it," demands Peter.
"No can do," says the Shaper. "What I shape, remains shaped." And he disappears.
Peter goes back to Queens. What can he do? He can't tell anybody. And — now that he's met the Shaper, he's finding those little tickles are starting to disappear. Like they're being erased. Like he's forgetting that things used to be different.
By the end of maybe nine, ten months, the status quo would be the status quo, and no further mention would be made of the Shaper, or the previous timeline.
So basically they created Ultimate Spider-Man as well.
Sublime was the big bad guy in Grant Morrison's run on New X-Men. A sentient bacteria that has existed as long as life has, possessing various bodies and trying to destroy mutantkind. Sublime still exists and is the basis for current X-Men storylines by Matt Fraction and Kieron Gillen.
Of course, decades earlier, John Byrne had created That Which Endures in West Coast Avengers, a sentient bacteria that has existed etc etc… and also has issues with mutants.
And now of course we are faced with a death in the Fantastic Four. You know, if it's Reed Richards Marvel have to be doing it on purpose.