The New X-Men was the training team of students at the Xavier Institute for Higher Learning. After the student body was ravaged by M-Day only a select few were chosen to make up the team, rather than the squad system the school had used. The team was broken up after the closing of the Institute.
William Stryker and the Purifiers
After M-Day cost most of the Xavier Institute's students their powers, Cyclops and Emma Frost decided that it would be too dangerous to keep the de-powered mutants at the school. They arranged to send them home by bus, but to avoid potential hostility the move would be made at night. The bus was struck by a missile fired by the Purifiers, killing the former students and sending shockwaves through the remaining students. Emma Frost decided to train a select group of students specifically for combat and had the students fight each other in the Danger Room, picking Dust, Elixir, Hellion, Mercury and Rockslide for her team. Cyclops, who was not amused by Frost's actions, placed X-23 on the team as well. Shortly thereafter, Elixir was removed from the team after attacking Colossus during a training exercise.
The Purifiers, believing themselves to be doing divine work, had a glimpse into the future through the remains of the Nimrod robot, and William Stryker used these visions to unleash attacks on the Institute. With the help of Icarus, who had been tricked into aiding them, the Purifiers killed Wallflower with a sniper shot and lured Dust (actually a disguised X-23) to their headquarters to kill her as well. With his usefullness expended, Icarus himself was killed, using his last strength to try to warn the others about Nimrod.
The Purifiers attacked the school, injuring several X-Men and killing student Quill, but the New X-Men struck back with Dust severely scarring Matthew Reismann and Elixir killing William Stryker. The aftermath left a deep hatred for the Purifiers in the students and Elixir in a catatonic state after using his powers to kill rather than heal.
While in Salem Center, Mercury and X-23 were ambushed by X-23's former captors of the Weapon Plus program and captured. Using a piece of Mercury's liquid-metal body, they coated their genetically engineered monster Predator X with a similar shielding and set it loose. While the other students and X-Men arrived to rescue their friends, Predator X escaped and began hunting mutants at random.
Detecting the presence of Illyana Rasputin during the events of House of M, the demon lord Belasco kidnapped the students who had been with her, bringing them to Limbo and demanding to know where she was. The students, having no recollection of the House of M events, cannot answer him, so he begins torturing them - reducing X-23 to bones and ripping Prodigy's heart from his chest, though Elixir managed to save them both.
Another group of students elsewhere in Limbo located a soulless Illyana, who convinced Pixie to give up her soul to create a new Soulsword - the only weapon capable of defeating Belasco. Anole stopped the process, with Pixie only losing a part of her soul and getting a Soul Dagger for her efforts. As a rescue effort comes into Limbo to save the students, Pixie defeats Belasco with her new weapon and Illyana, flooded with memories of her old life, sends the group home. Impressed by their efforts, Cyclops allows Pixie and Anole to officially join the team.
When the X-Men learned of the new mutant birth in Alaska, they purposely left the New X-Men out of the mission teams, knowing they would want vengeance against the Purifiers, who had become involved. Their fears were justified, as Surge gathered the team and prepared to attack and rescue the baby. Elixir, Dust and Prodigy declined to participate, but the others made a quick strike into the Purifiers base. Anole found that they did not actually have the baby and also that Cyclops had sent Rictor to infiltrate the group. Rictor told him to get the kids out quickly, but his warning came too late. Lady Deathstrike and her team of Reavers had allied with the Purifiers and began taking the kids apart. In panic, Pixie teleported the team out blindly, scattering them over a distance and inuring herself in the process. Iceman recovered the kids and brought them back to the ravaged Institute, but the cost had been heavy. Hellion had been severely injured by Deathstrike and Elixir had been knocked unconcious by a Sentinel attack on the school, preventing him from healing his friends.
While the X-Men battled the Marauders over the baby, the recuperating New X-Men were found at the mansion by Predator X. Pixie, remembering that X-23 had killed one of the creatures before, attempted to teleport it to her location, but ended up sending the students and a group of the injured to the battlefield. After the battle, Cyclops decided to close the Institute, disbanding the team and sending the kids home.