Sabretooth wrecks havok in New York City, stirring anti-mutant hysteria. The news reports draw the attention of Jubilee’s foster parents, terrified for her safety. Jubilee overhears her parents arguing over registering her with the “Mutant Control Agency”. Upset, she leaves the house and heads for the mall. Meanwhile, a Sentinel is on her trail after finding out she’s not in her room.
Jubilee fries a video game at the arcade in the mall and is chased out by the manager. She runs into Storm and Rogue. The Sentinel barges into the mall and captures Jubilee. The X-Men, Storm, Rogue and Gambit come to her rescue. The Sentinel takes out the X-Men with stun blasts. Jubilee makes a run for it out of the mall. The Sentinel chases after and gasses her unconscious. She runs into Cyclops who takes out the Sentinel.
Jubilee is taken to Xavier’s School for the Gifted where she comes across the other denizens of the mansion such as Beast and Morph. She enters the War Room where the Sentinel head is laid out for examination. She senses people entering and leaves as she tries to find a way to escape. Professor Xavier alerts the X-Men to her escape.
She enters what turns out to be the Danger Room where Gambit and Wolverine are training. Thinking that Wolverine was going to hurt Gambit whom she met at the mall, Jubilee stuns Wolverine with her powers, ending the training session. Beast and Morph find the situation amusing.
Storm takes Jubilee on a tour to “explain who [they] are”. Meanwhile, Xavier has a discussion with the X-Men. The private organisation, the Mutant Control Agency is planning to track down and eliminate mutants with information from their database. Xavier wants the X-Men to destroy the agency’s database.
Jubilee rushes home to check on her parents. She is ambushed by another Sentinel and apprehended.
The X-Men are separated into different teams to penetrate the agency. Cyclops questions Xavier as he is reluctant to have to use his powers against humankind as they were trained not to do. He is subsequently taunted by Wolverine but the squabble is broken up by Jean who comes to alert Cyclops that Jubilee has escaped. Wolverine is insistent on saving Jubilee instead of going on Xavier’s mission.
Cyclops, Storm, Beast, Morph, Rogue and Gambit arrive at the facility by the Blackbird. Wolverine joins them at the last minute. Storm creates mist to cover their intrusion. Cyclops, Rogue and Gambit remain outside as the lookout.