We join Jubilee on a cold, Christmas Eve morning at the Massachusetts Academy. She hates Christmas. She is an orphan.
Meanwhile, a young boy named Matthew is being bullied by a group of his class mates. The ringleader, Stephen, forcefully takes Matthew's money and leaves him on the floor, but as the crowd walk away, Matthew's mutant abilities activate and he telepathically pushes them all away. The crowd run off, calling him a freak.
In a cottage in the woods, the mutant child kidnapper, Nanny, is baking cookies for Peter - The child-like Orphan Maker. He is writing his Christmas list, when Nanny reminds him that they have their Christmas tradition to take care of first - to orphan a mutant child. Peter tells her he is worried that she might like the new orphan better than him, but Nanny tells him that he was her first orphan and will always be special.
Skin, Synch, M, Jubilee, Husk and Chamber are last minute shopping. Husk is feeling sad because the airports are shut and she cant get home to Kentucky to spend Christmas with her family. Chamber consoles her and she cheers up a little.
Matthew hears his parents talking about him, but he has hatched a plan that will make everything better. He hides behind the couch and waits....
En-route to make a new Orphan, Orphan Maker detects a surge of mutant signatures in the Mall and investigates. He finds Generation X, and remembering them from the last time they fought, attacks. Gen X manages to clear the Mall of civilians, but are captured when the Orphan Maker uses his Pixie Dust to knock them out. Nanny is proud of the five new mutants, but sends Peter out again, as he still has to make a new orphan.
Jubilee is trudging home in the snow angry because she thinks the others left without her, when she sees the Orphan Maker. He lands at his destination, but he can’t narrow down the mutant signatures, and accidentally enters Stephen's house. As he is about to kill the parents, Jubilee stops him, but Orphan Maker manages to grab Stephen and escape. Jubilee is thrown onto Matthew's roof where she finds Santa's reindeer. She falls down the chimney in shock and finds Matthew with Santa Claus strapped to a chair. Thinking she has gone mad, she tries to get up and leave, but Santa reads her Matthew's Christmas letter, where he asks Santa not for gifts, but to be normal again.
Nanny realises they have the wrong child and when Stephen asks if he can go she tells him that he will have to become a 'Lost Boy'. She again sends Peter out to retrieve the right boy as Gen X manage to free them selves and attack Nanny.
Matthew admits to holding Santa to get back at Stephen, because he knew if he detained Santa, then Stephen wouldn't get any presents. Jubilee tries to reason with him as his powers dont work on other mutants. Then, Orphan Maker finally gets the right house and attacks Jubilee and Matthew, but, when he sees Santa he forgets his mission with all the excitement. Santa explains that Peter has been a bad boy, but could put things right - but he hears Nanny's pleas for help and returns to her. Santa gets up to leave as he has the rest of his rounds to do and Jubilee wonders if Santa is really a mutant as he was never really restrained.
Gen X return Stephen to his house and when he starts being nasty about Matthew again, Synch tells Stephen that he is in fact a mutant too (Stephen isn't really - Synch just said that to scare him a little)
Peter returns to the cottage to find a very angry Nanny and Jubilee and Santa have a heart to heart and he rekindles to spirit of Christmas within her. Jubilee awakens on Christmas Morning feeling happier than she has in many years.