The novel concerned a minister, the Reverend William Stryker, stirring up religious anti-mutant fervor and kidnapping Professor X in an attempt to eradicate all mutants. It is one of the most clear-cut examples of X-Men comics using mutant relations as a metaphor for race relations.
It's the first appearance of William Stryker in X-Men's titles, a continuous enemy of the team in the future.
The novel begins with two young children running away from Purifiers in a school. They are caught, shot dead and left behind tied up with the word muties. Magneto finds them before the sun rises and promess to himself that he will make them pay for that.
At ABC Late News we watch a debate between Professor Xavier and Stryker about the mutant issues, and Stryker manages to convince everybody about his racists thoughts. When Xavier, Ororo and Scott are riding back home after debate, they are attacked by some Purifiers, they are shot and the car is blown away.
The others (Colossus, Kitty, Nightcrawler and Wolverine) susceed in a training session at Danger Room programed by Peter's sister Illyana (who is still with the X-Men after being kidnapped by Arcade at Uncanny X-Men #145). Then they get a call informing that Professor X, Storm and Cyclops are dead. While Kitty and Illyana stay at X-Mansion, the others go to the Central Park investigate the deaths. Wolverine senses that the burned bodies aren't from their friends and then they are attacked by some Purifiers at the street. When they would be defeated, Magneto showed up and help then, arresting the soldiers in a metal cocoon. Magneto and Wolverine torture the soldiers and get information about Stryker cruzade agains mutants. Back at X-Mansion, Kitty and Illyana are also attacked and kidnapped by some Purifiers's soldiers.
Meanwhile, Stryker is torturing Xavier trying to mind control him. Stryker tells us about his past, when he was Sargent of the Rangers, he had a baby mutant (with some kind of monster looks). He decides to kill his wife and the baby. He starts to drink, is expelled from US Army and then gets knowing about Xavier and the mutants. Suddenly he reallizes that the mutants are the evil and he had to destroy them all, in a cruzade in the name of God.
Kitty manages to escape from the trunk she was hidden and calls Nightcrawler. When she was about to get killed Magneto, Colossus and Wolverine show up and rescue her.
Stryker susceeds on mind controlling Xavier and makes him kill Cyclops and Storm. Kitty and Nightcrawler kidnapp Stryker and ask for informations about their friends. Then the X-Men and Magneto rescue Cyclops and Storms bodies, just in time to realize they are alive and Xavier still has got some control on his acts.
At Madison Square Garden, Stryker is making a huge talk about how the mutants are monsters and the humans have to make something about it. Then he uses Cerebro and Xavier to locate and kill all the mutants on Earth. Magneto shows up at the Garden, but Xavier attacks him with a huge mental blast and almost kill him. The X-Men enter from the backstage and defeats the guards. When Stryker reallizes one of his soldiers is a mutant, he push her and got her killed. Some people around starts to doubt about Stryker, but others shout that it's all mutants fault and try to kill Magneto, but are stopped by a couple cops. Cyclops makes a plan to attack Xavier using Nightcrawler and Wolverine and at the end they susceed on knocking Xavier unconscious.
The X-Men show up to the crowd and confront Stryker. Cyclops says that the mutants are humans just like everybody with some special skills, like athlets or doctors or scientists. Stryker points at Nightcrawler and asks if he is also a human king, and Kitty says that he is more human than Stryker, who points a gun on her. When he is about to shoot Kitty, the policeman shoots him.
At the end, at X-Mansion, Magneto ask the X-Men and Xavier to join his cruzade against the humans and their hate, Xavier accepts, but not Cyclops, who still believes on his dream of humans and mutants living together as one unique race. Magneto flies away wishing good luck to them, because if they fails he won't.