Scarlet Witch
She is ashamed of what she has done as it lead to the death of her father Magneto, and her brother Quicksilver. She wants to make amends but almost every mutant wants to see her dead. She now lives in exile within Alaska.
Jean Grey/Hope Summers
These two Omega level mutants combined their powers to channel the Phoenix. The Phoenix destroyed the virus the day after it was released. Unfortunately the Legacy Virus was so powerful that Jean Grey and Hope Summers had to sacrifice themselves to stop it and as for the Phoenix Force, it has been weakened to the point where it can no longer possess others and hasn't been seen since.
Storm
Unfortunately she was afflicted with the Legacy Virus and died. She is buried in Wakanda in the royal cemetery.
Cyclops
He was depowered by the Legacy Virus but Purifiers found him and killed him before the virus overtook him completely.
Wolverine
The Legacy Virus took away his healing factor. His enemies immediately swooped in for the kill. Wolverine managed to kill his nemesis Sabretooth before Lady Deathstrike killed him.
Domino
The Legacy Virus began affecting her on the day after it was unleashed. She managed to shift the odds in her favor before her powers were lost and was able to survive. She is no longer an active member of the X-men. Instead she trains young mutants how to use weapons to protect themselves against the Purifiers.
Gambit
Gambit survived M-Day but he was separated from Rogue. He does not know if she survived or not and he does not know about Rogue's secret.
Mystique
She survived M-Day but her current whereabouts are unknown.
Beast
It is unknown if he survived or not. His lab has been found abandoned and the remaining X-men fear for the worst.
White Queen
She survived and started a new X-men school, Frost's Academy of Higher Learning. She serves as the school's headmistress. Dr. Kavita Rao and Dr. Cecilia Reyes are Resident Physicians at her school.
Rogue
She survived M-Day. She was separated from Gambit during M-Day and is desperately trying to find him. She was asked to be a staff member at Emma's new school. She accepted and helps teach mutants how to control their powers.
Warbird
Kid Gladiator returned to his home but Warbird stayed behind on Earth. She serves as the Art instructor at Emma's school.
Psylocke
She survived M-Day and is an instructor at the new X-men school.
Shadowcat
She survived M-Day and is the Vice Principal at the new X-men school.
Rachel Grey
She survived M-Day and is an instructor at the new X-men school.
Archangel
He survived M-Day. He is the flight instructor at Emma's school.
Armor
She survived M-Day and now works for the White Queen's school as a recruiter with Pixie, and Nightcrawler. They roam the U.S. trying to find new mutants before the Purifiers do.
Magik
Illyana died early on when the Legacy Virus was unleashed.
Iceman
He died shortly after Magik did.
Dazzler
Purifiers ambushed her after one of her performances and killed her.
Firestar
Her powers burned out and the virus overtook her soon after.
Blink
She died on a mission for the Exiles.
Magma
She survived M-Day and is an instructor at the new X-men school.
Karma
She survived M-Day and is an instructor at the new X-men school.
Colossus
He survived M-Day and is the combat instructor at the New X-men school.
X-23
She survived M-Day and joined the Avengers.
Hellion
He survived M-Day and joined the Avengers. He is dating X-23.
Oya
She survived and is currently a member of the Avengers.
Transonic
She survived and is currently a member of the Avengers.
Mercury
She survived and joined the Avengers.
Surge
She joined the Avengers.
Primal
He died of the Legacy Virus.
Rockslide
He is a current member of the Avengers.
Velocidad
The continued use of his powers led to his death as he aged far too quickly.
Mister Sinister
He survived M-Day. His lab is gone and he has start again from scratch. See Dark Genesis for details.
Madelyne Pryor
She survived M-Day. Pryor is building a new Sisterhood of Mutants. See Dark Genesis for details.
Students
This is the list of canon students that currently attend Emma's school:
Blindfold/Ruth Aldine
Cipher/Alisa Tager
Crosta
Dust/Sooraya Qadir
Eye-Boy/Trevor Hawkins
Gentle/Nezho Abidemi
Indra/Paras Gavaskar
Match/Ben Hamil
Nature Girl/Lin Li
Rico
Shark Girl/Iara Dos Santos
Sprite/Jia Jing
Trance/Hope Abbott
There will be some OC students but most of them will not be introduced until a later book. If you want to submit an OC student for the school, Feel free to PM me.
*****As a disclaimer, this list is subject to change as mutants may be added or have their fates changed. If there is a mutant that is not on this list and you want to know their fate feel free to PM me.