In the sewers beneath New York, Masque and some other Morlocks kidnap Leech and hurt Caliban. As Nightcrawler and Professor X talk, Hepzibah and Warpath have a little training session outside. Caliban turns up on the grounds badly injured, but before ONE can take him in, Storm shows up and puts Caliban under her protection.
Professor X and Nightcrawler plan to go and find Magneto, while Warpath, Hepzibah, Storm and Caliban enter the sewers. They find a precognitive book written on a wall, displaying possible outcomes for the future. The Morlocks unleash a bomb a Bliss’s venom, knocking out a train full of people, while Masque mutates the people.
Masque broadcasts his attack all over the internet, while Professor X and Nightcrawler continue to look for Magneto. Storm and the team use the Baxter Building’s map of New York to look for possible hiding places of the Morlocks. They enter a building to find a bunch of SHIELD agents dead, and Skids buried under rubble, revealed to be an agent of S.H.I.E.L.D.
As the team fight a Sentinel, Nightcrawler and the Professor continue to search for Magneto. The team decide to go back into the sewers to find the Morlocks. After splitting up, Warpath and Hepzibah are caught by the Morlocks. Storm, Skids and Caliban visit a group of followers of the book when the roof collapses and leaves them trapped.
The Professor and Nightcrawler arrive a bit to late to help the team who have been captured by the Morlocks. Masque prepares to kill every person in a church above when Storm breaks free, and frees the others, and they beat the Morlocks. Skids takes the precognitive book (written by Qwerty) and gives it to Magneto: With a rhetorical question leaving us to wonder whether Magneto has his powers back or not.
Issues 488-491 include chapters 2, 6, 10 and 14 of the Endangered Species crossover.