The X-Tinction Agenda begins as the nation of Genosha declares war on the X-Men. Alex Summers leads a team of Magistrates against the New Mutants and the X-Men and take a few hostage. Just when both teams thought they could settle down... First Strike!

Trish Tilby reports that the Genoshan government is calling out the world in its attack on the X-Men. Genosha plans to negate the X-Men threat and hopes the world will be sympathetic. At Xavier's, Banshee, Stevie Hunter, and Forge watch as Jean Grey and Storm duke it out in the Danger Room. They want to see how Storm's new teen-aged body will handle fighting an adult. At first, Jean has the upper hand. Storm, however, has been sneaky and catches Jean off guard with an ice attack, coupled with a whirlwind. Stevie cancels the practice just in time; Storm's powers have been completely taxed and she falls to the ground. Jean catches her as Cable barges in with the New Mutants. An argument breaks out due to different leadership styles, but Storm steps in and mediates. The X-Men leave the New Mutants.

At Lila Cheney's, Fred Stanachek tries to get past Guido to see Dazzler. Guido says she's not there, even if Fred only wants to talk about the hit movie of Dazzler's. Guido lectures the guy on knowing when to let go and physically moves Fred's car. As Fred drives away, a bright flash manifests from the beach. Guido investigates to find Lila Cheney having returned. Her words are ominous: Professor Xavier is in danger.

In Harry's Hideaway, Storm and Jean relate their personal struggles with their identities. Jean has had too many extensions of herself: the Phoenix and Madelyne Pryor. Storm has been reduced to a state of adolescence, but a kind in which she never progresses. Unbeknownst to the two, Genoshan Magistrates are spying on them. Back on mansion grounds, Storm bids Jean good-bye. From the shadows, Wolfsbane confronts Storm. Wolfsbane is bitter that the X-Men are safe and sound while her friend, Doug Ramsey, had to die. Storm explains that some decisions aren't always the best, like the X-Men being in hiding so as to strike at their foes at unawares. Wolfsbane storms off and Stevie asks if Storm plans on stepping aside as the X-Men leader.

Just then, Genoshan Magistrates attack with their prime directive being the hatch to the underground complex. Boom-Boom, Wolfsbane, Rictor, Storm, Warlock, and Stevie are all pursued above ground as the alarm in the bunker sounds. Storm and Stevie reach the hatch as one of the magistrates calls reinforcements. Pipeline ports the rest of the forces directly to the bunker hatch. Storm shoves Stevie through and into Cable's arms and then seals the hatch, locking everyone inside while trapping the aforementioned mutants up top. Cable gets angry and he and the rest head towards another exit so as to help against the attack. As Storm leaves the hatch, she notices a magistrate using a self-generated blast. She recognizes the power signature. She steals one of Boom-Boom's time bombs with her wind and directs it at the magistrate using the power blasts. The magistrate ends up being Havok, a former X-Man. Storm tries to lead the mutants, but Boom-Boom and Rictor get caught, shortly followed by Warlock. Wolfsbane and Storm are next. Pipeline teleports the mutants to Genosha. Cable and his group finally reach the surface but can only surmise that the kids have been teleported away.

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