Generation X is formed, and all the members meet their new sanctuary, and also get to see their own "danger room." This issue also marks the debut of the new mutant Chamber, whose arrival in the United States is greeted by the mysterious new enemy Emplate who feeds on mutant bone marrow.
Paige Guthrie, a new student at Xavier's Institute of Higher Learning, jogs in the early morning preparing herself to be the absolute best. Intending to be a leader, she wants to set an example for her new peers.
Paige's enthusiasm and drive, however, had awoken fellow student Jubilation Lee (also known as the X-Men's Jubilee). Dressed in big, fuzzy house slippers, pajamas, and her famous yellow trenchcoat, Jubilation rants about her lack of sleep and "hayseed"'s loud workout video that blasted in the early hours of the morning.
Paige brushes off Jubilee and readies for class. With her mutant ability to shed her outer layer of skin in favor of a new one, Paige cleans herself up by shedding her sweat with a fresh new epidermis. Grossed out, Jubilee recalls her time with the X-Men until she is interrupted by Monet St. Croix who lands from a brief flight.
Monet St. Croix, whose abilities range from self-propelled flight to incredible strength, is a very confident and sarcastic young woman. Jubilee warns Monet about using her powers in public, but Monet brushes off her concerns. The two begin to argue, but they are interrupted by their headmaster, Sean Cassidy (also known as the mutant superhero Banshee).
Monet informs Mr. Cassidy that she is expecting a few of her belongings to arrive. He puts it upon himself to take care of the luggage, but is surprised when he finds several trucks head into the driveway.
Elsewhere, Jonothan Starsmore, covered in black leather with a scarf covering his mouth, is making his way to the school from his home in England. A curious passenger sitting several rows away from Jono watches from afar. Jono re-reads his letter from Professor Xavier and wonders what can really be done for someone who is so far removed from normal.
Back at Xavier's, Everett Thomas (Synch) searches for his opponent in a jungle-like environment. He finds Angelo Espinosa (Skin)'s X-belt medallion in the shallow end of one of the swamps. Concerned, he begins to call out for his opponent, fearing for his safety. In the darkness of the shrubs behind him, Angelo's fingers begin to stretch and he grabs Everett from the ankles. The two begin to have a friendly tussle, until Angelo becomes concerned about his skin. Angelo is still getting used to his mutant powers and worries about his skin tearing. Everett is able to copy the powers of mutants within his vicinity and takes on Angelo's abilities.
Nearby the three girls--Jubilee, Monet, and Paige, walk through a metal room with a view of the jungle environment. Sean Cassidy explains that their first training session will be in this bio-sphere. Paige is alarmed after having studied the layouts and scenarios of the Danger Room she was eagerly prepared to endure. Sean remarks that the terrarium is a superior upgrade to the Danger Room and that it is as safe as can be.
Cassidy bites his tongue as Everett and Angelo plunge through the window after their friendly training session turns into an all out brawl that neither seems willing to concede defeat. Cassidy breaks up the fight and asks who would dare think it was a good idea to pit student against student when they lacked the training that was needed.
In walks headmistress Emma Frost, former White Queen of the infamous Hellfire Club. The two begin to argue over their plans for the students. While the two argue, the students wander off. Jubilee notices something through the whole Everett and Angelo made, but brushes it off as nothing.
Later, Jubilee and Synch prepare to pick up their new student from the airport. Monet, while climbing a tree, overhears the two converse and feels above doing Xavier's work for him. As the pair head off with Banshee, Monet encounters Gateway, a mysterious old Aboriginal mutant with the ability to create portals that can teleport several people across long distances.
Monet acknowledges Gateway as her mentor. She's excited to see him, but insists she continue her learning experience with the mentors of the X-Men. Without words, Monet realizes that his arrival has little to do with her, but with someone else. Someone they both know and fear has returned.
At Logan International Airport in Boston, a sinister car awaits for Jonothan Starsmore to arrive. The passenger in the back, Emplate, knows that a freak like Starsmore has no worth to anyone but him.
Emplate walks throughout the airport, seemingly undetected. Emplate senses a mutant aura in one of the older gentlemen in the airport. But no, he requires someone more vital to feed on. Deep within his soul (or what's left of it) he can sense a powerful mutant in the distance.
Nearby, Generation X's trio of mutants wander the airport looking for Jonothan's exit. The two younger students discuss Everett's sympathy with what humans must feel about mutants. He realizes that between the three of them alone they could wipe out the entire airport and yet go seemingly undetected.
Both parties then catch a glimpse of Jonothan, whom Jubilee calls "the walking band-aid". Emplate grabs Jono and begins to feed on him. People begin to panic and Jubilee saves a young girl who can't escape Emplate. Banshee utilizes his mutant powers and gives a big sonic scream targeted at Emplate to release Jono.
Emplate analyzes his competition closely. While he siphons energy from Jono, he also reabsorbs the blast Banshee projected towards him as well. Synch jumps into the blast, mimicing Emplate's ability to absorb the power as well.
Meanwhile, Jono seems to be able to utilize his power while under Emplate's grasp, a first in the demonic mutant's experience. Jono emerges from the ground with his scarf no longer concealing the bright psionic fire that ignites from his mouth to his abdomen. As both parties are impressed and Emplate prepares to feed once again, Emplate falls to the ground from an unexpected hit that surprisingly injures Emplate.
In comes the rest of Generation X--Monet St. Croix, Husk (Paige Guthrie), Skin, and headmistress Emma Frost--teleported in by Gateway. Emplate is caught off guard by the blow from Monet, as well as the fact that she knows his name. Husk dashes towards Emplate ready to attack, and Banshee screams out to her as he remembers his first mission with the X-Men when his teammate Thunderbird (John Proudstar) was killed.
The rest of Generation X had already lost one of their own on a previous mission (Clarice Ferguson aka Blink) in a battle against the Phalanx. As Husk lays injured on the ground, Banshee directs Monet to take Husk to the nearest hospital. However, Jubilee quickly recalls the nature of her teammate's mutant abilities and hesitantly begins to rip the injured layer of skin away, reducing the injuries and bringing Husk back to consciousness.
As the rest of Generation X regroup, Emplate prepares to leave before giving one last threat to the team. He proclaims that he will return and that he will find every last one of them until he has fed on them all.
Before he fades away, Monet tries to go after him before being frozen in her place. Emma Frost telepathically commanded her to stay in place as to not experience a similar setback that had happened to Husk only moments ago.
Monet angrily protests for Emma to never invade her mind again. The two argue while Emma psychically makes them invisible to the rest of the people in the airport so that the team can leave.
Jubilee introduces herself to Jonothan and welcomes him to the team.
Far away in an undisclosed location, Emplate and his driver, D.O.A., are back in their mansion. Emplate abrasively avoids conversation about what had happened and instead wants to feed on a continued source of sustenance he has trapped in a room. He's alarmed to see that she had escaped and the pair are determined to bring her back.
Back at the Xavier Institute, things are still uneasy amongst the group, especially between Banshee and Emma Frost. Jonothan enters the room and alerts Sean about a visitor waiting outside. Banshee quickly tells the students to stay inside as he sees to their guest. He finds Gateway sitting in the yard. Irritated by his mysteriousness and indirectness of his motives, Banshee begins to argue with the very quiet mutant who finally speaks the words "Penance". Emma comments that he's referring to a young red mutant wrapped in leather straps laying unconscious on the front lawn.
The issue also contains a sketchbook with brief descriptions of Penance, M, Jubilee, Skin, Chamber, Husk, Synch, and Mondo (who had yet to make his proper debut).
This issue marks the true first appearances of Chamber and Penance, despite the fact they were previously seen in preview material leading up to the release of Generation X #1.
The M Twins did not appear in this issue, unless you count the fact that they were masquerading as their older sister M. However, it then stands to reason that they appeared as M.