When Gene Nation members Marrow and Hemingway capture Generation X headmistress Emma Frost in the underground sewers of the city, her young students must come to her rescue before its too late.
Before they even finish formulating their plans, their crafty teacher escapes capture and defeats her kidnappers with rather ease.
Watching from afar, the devious mutant the Dark Beast plans an attack on Frost and her team of young mutants for interfering with his mysterious plans and causes planted explosives to detonate around the perimeter.
The team luckily escape and take refuge at Xavier's Institute. There, Jubilee reunites with her former mentor, Wolverine, who has taken on a more dangerous and feral form. He encourages her with words of wisdom to remain with her team to learn to further control her mutant abilities.
Elsewhere, Husk unwinds after a night of drinking with the help of her teammate Chamber. For reasons unknown, Chamber destroys the girls dormitory.
Generation X co-leader Emma Frost finds herself captured by Gene Nation members Marrow and Hemingway. Painting her body with orange paint to demean her, the pair are using the young mutant power sapping child Leech to keep the powerful telepath from using her powerful psychic abilities to escape and defeat them.
Marrow has heard stories of the infamous White Queen, but Emma insists she's a changed woman now and merely a instructor for the next generation of mutants. Emma condescendingly offers the two mutants to join her school for lessons in refinery, an offer which makes Marrow very hostile and threatening. Emma Frost keeps her cool the entire time and maintains her sarcastic wit.
Elsewhere, the students of Generation X--Synch (Everett Thomas), Jubilee (Jubilation Lee), Skin (Angelo Espinosa), and young Morlock Artie Maddicks search for their teacher and mentor. While they tried contacting the X-Men for assistance, the students know that there may not be enough time to wait and depend on their help. Skin is rather annoyed by the natural affinity Artie Maddicks has for him as he carries him on his back through the sewers.
Synch uses his powers to track down their mutant energies and when he catches a lead the other students follow.
The students arrive to the scene and watch from above the ceiling as Emma Frost banters with the two members of Gene Nation. Marrow reveals that she killed several people at a disco because they were fortunate enough to live above ground and be merry while her people--mutants, specifically the underground Morlocks (a group from whom Gene Nation is an off-shoot of), were forced to hide in shame in the sewers.
Hemingway wants to do away with Frost quickly, but Marrow refuses until the "First One" arrives.
The three hidden students know that Leech's powers have also dampened their mutant abilities, but before they can conjure up a plan, Emma Frost swings from the ropes she was tied from and kicks the Leech in the face, knocking him out and turning out his power along with his consciousness.
Emma then uses her powerful telepathic abilities to mind fry the her two kidnappers.
It is revealed that the entire event was being watched on television monitors by the Dark Beast, who was Marrow had referred to as the "First One". He is upset by the shrinking number of Morlocks he could do genetic experiments on and is angered by the interference of Generation X. With the press of one button, he causes the sewers they are in to explode.
Fortunately, the kids are all safe. Jubilee tries to rescue Leech, who is buried underneath the rubble, but is greeted by Monet St. Croix (also simply known as M) who has beat her to it.
Generation X heads to the Xavier Institute to recuperate. There Jubilee reunites with Wolverine, who has undergone an extreme feral state since losing his adamantium. He warns Jubilee to stay in school to be fully aware of her powers so that she doesn't experience what he is currently going through.
Back at the Massachusetts Academy, Husk is getting over a hangover from a late night of drinking. Chamber watches after her as after she vomits and seems to be stressed out over a new revelation about the Legacy Virus.
Moments later, the girls dormitory explodes. Generation X mentor Banshee knows it can only be one person who caused the disaster: Chamber.