Along with search and rescue crews, Beast and Jean search for survivors in the decimated country of Genosha. Due to the extreme radiation levels, they wear oxygen masks to prevent contamination. No one finds anything but ruined buildings, skeletons, and corpses until Jean detects thoughts underground. She and Beast remove at least 50 tons of debris to find Emma Frost, coated with an exoskeleton of diamond and carrying the dead body of one of her students. The search and rescue crews take the body away and Jean tries to comfort Emma, who has a hard time dealing with the chaos. Everyone notices Emma’s hard skin, which she never had in the past.
In the Xavier Institute, Professor Xavier, Cyclops, and Wolverine listen to news reports claiming that more than half the world’s known mutant population has been wiped out due to the ethnic cleansing in Genosha. The X-Men decide to stop the sentinels and mobilize more emergency squads, but they wonder what to do with Ms. Nova, whom Cyclops and Wolverine apprehended and brought back with them from Ecuador. Ms. Nova is imprisoned, afloat in some kind of a pear-shaped containment unit that radiates green light. Wolverine mentions that he severed her vocal chords to prevent her from voice activating more sentinels, but her own healing factor will fix the damage soon.
Beast examines Emma in another room of the mansion, analyzing her new ability, which he calls “an exoskeleton of invulnerable organic jewelery.” He tells her that she has some type of secondary mutation and she replies that she’s never heard of such a thing, but Emma accepts her newfound power nonetheless. Emma wants Ms. Nova to die for her atrocities, but Jean says death is too extreme. Jean asks Emma for help on the X-Men’s behalf, but Emma rebuffs her, thinking the X-Men too passive. Emma telepathically calls a taxi so she can leave.
The X-Men gather round Ms. Nova’s containment unit to decide what to do with her and what her motivations are. Beast reveals her full name, Cassandra Nova, and says that even though she looks human, she’s neither human nor mutant, something else entirely. According to Beast, Cassandra is “the first of a new unforeseen species” and wants to wipe out mutants because they’re a threat to her kind on the evolutionary food chain. He also says that the human race will become extinct within three or four generations due to the mysterious E-gene. The gene is “a genetic trigger for extinction buried deep within the human genome” that activates when an entire species is about to disappear. The E-gene marks humanity’s end, leaving only mutants or creatures like Cassandra to inherit the Earth. Wolverine wonders why she looks so much like Professor Xavier, but before Beast can address him, Cassandra breaks free of her containment unit and attacks the X-Men. Using tremendous telepathic and physical abilities, she ambushes them and makes her way to another part of the mansion.
Outside, Emma rides away from the Xavier Institute in a taxi, minus her diamond hard skin and talking with the cab driver. After an epiphany, she decides to return to the mansion and tells the driver to stop the car.
Meanwhile, Cassandra is successful in fending the X-Men off while she makes her way through the mansion. Professor Xavier deduces that she’s trying to reach Cerebra so she can augment her power. Cassandra reaches Cerebra and dons the machine’s helmet. She mentions that, though she can telepathically eradicate every mutant brain on the planet through Cerebra, she only wants to affect one in particular. Almost on cue, Emma arrives and takes Cassandra by surprise, snapping her neck. This time Emma has her hard exoskeleton, apparently able to control when it comes on or off. Despite the attack, Cassandra’s body begins to heal. She tries to talk “Auum ... Umma ... Ummmmm Charles ... Nuuuuu ...”, but Professor Xavier shoots her several times to make sure she dies, splattering the room with bright blue blood. Then he calls the X-Men to him and mentions that things should change.
Later, Cyclops and Jean have a discussion while watching Professor Xavier on a television talk show. According to the news, surprisingly, many people have sympathy for mutants after the Genoshan attack. The entertainment industry plans on “changing stereotyped portrayals of mutants in movies and on T.V.” Cyclops and Jean talk about the distance in their marriage and Professor Xavier’s strange behavior. Cyclops has been feeling differently about some of his beliefs and values due to his recent battles with En Sabah Nur in his head. He has doubts about who he is and where that leaves his relationship with Jean, but Jean assures him those feelings will pass with time. She believes the bond between them is too strong to break. Then the two of them are stunned as they watch Professor Xavier come out on television, letting the entire world know that he’s a mutant.