As the X-Men make their way onto Genosha, Wolverine and Carol Danvers (in control of Rogue's body) try to sneak around the country bent on finding them. They trail the Genegineer's son and discover more atrocities than they cared to know about. Meanwhile, Madelyne's mind is probed druing the mutate bonding process, which unleashes a powerful psionic pulse that kills everyone around her.
The Genegineer and Chief Magistrate Tam Anderson lead a remote operation in which field Magistrate’s try to overtake a stolen aircraft. The craft won’t pull over so a Magistrate jumps atop the flyer and pries the hatch open. The hatch is rigged, however, and the craft explodes. Nobody was even inside. The Genegineer is not pleased, as he knows the two thieves, former prisoners Wolverine and Rogue, may have allies that will come to their aid at any time. Anderson commits to finding the escapees.
Outside a store, Wolverine watches a bit of propaganda about Genosha and all its splendors. He then turns to see a mutate being harassed by a Magistrate. Rogue/Carol switches clothes and now wears a revealing dress, her point is that she might get noticed, but nobody will look at her face. She and Logan enter a Magistrate bar, where by coincidence Phillip Moreau tries to drown his frustrations. Wolverine encourages a bar fight so as to steal Magistrate identification. Phillip has no chance against the Magistrates. They knock Phillip out and decide to teach him a lesson. They dress him up as a mutate and place him on a train leading to the mutate camp in the citadel. Rogue and Logan follow in their Magistrate disguises and hop the train as it departs.
The Genegineer talks to Jenny Ransome after she begins the mutate process. He explains how important the mutates are for the country; the whole economic systems depends on the cheap superhuman workers. Jenny asks if she at least will still be a healer, but the Genegineer refuses, her powers will be oriented in other direction. He orders her to be taken to the final processing.
Madelyne is examined in a psionic lab, as they still can’t figure out if she is a mutant or not. As a telepath tries to probe her she warns him to back off. A huge psychic backlash is unleashed.
The X-Men arrive on Genosha a countryside through one of Gateway’s portals. They run into some Magistrates and defeat them. Psylocke attempts some telepathy but just then receives the pychic backlash from the Citadel lab. At that point, the Genegineer arrives in the lab and finds it in ruins, Madelyne unconscious, and the scientist team dead.
Onboard the mutate train, Rogue and Wolverine find Phillip Moreau, but the mutates in the train aren’t to happy to see some “Magistrates“ in their midst. Right before a fight starts, the train stops at its destination. More Magistrates enter the train and they are surprised to see two of their own inside the train, but Rogue/Carol and Logan provide a good explanation. They claim to have discovered a ploy against Phillip Moreau, the Genegineer’s son, who was dressed up and placed in the train. The Magistrates order Rogue and Wolverine to take him to his father.