After the Eve of Destruction crisis, the Massachusetts Academy closed its doors. Professor Xavier requested Emma Frost to teach in Genosha for unspecified reasons. A new nemesis for the X-Men arrived in the form of Cassandra Nova, Xavier's twin sister whom he killed in the womb. The fetal Xavier recognized her as inherently evil, his own personal "mummudrai", and strangled her until she was delivered stillborn. Very powerful, Cassandra remained alive but weak, until decades later when she was finally able to create a psionic body. Cassandra Nova resurfaced in South America and activated a forgotten Master Mold, manufacturing immense Sentinels to attack Genosha. Magneto, alive but paralyzed from Wolverine's attack, could do nothing but watch as the entire island along with sixteen million mutants were exterminated.
Emma Frost appeared at first to be the only survivor due to her sudden mutation of diamond-hard skin. Many mutants around the world began mutating further and gaining new powers. Dr. McCoy labeled them as secondary mutations. Other Secondary Mutations noted were Phoenix's returned telekinesis and Beast's more feline appearance.
Cassandra Nova was brought into custody by Cyclops and Wolverine, but managed to break free at the Xavier Institute and switch bodies with Charles Xavier. In Xavier's body, she shot her previous body to near death. At this point, Emma Frost officially joined the team and the Institute was reopened to students, containing a much larger student body and classes taught by X-Men. On live television, Cassandra Nova-as-Xavier admitted to the world he and all resident at the Institute were mutants, revealing the X-Men's best kept secret. Only the Beast suspected anything was wrong, and Cassandra Nova took control of Beak and had him beat him into a coma before she left on Lilandra's starship for the outer reaches of space.
Jean Grey assumed the role of Headmistress at the Institute and promptly drove off an attack by the U-Men; humans who graft mutant tissue to themselves. During her defense of the school, Jean manifested the Phoenix raptor. Meanwhile, Cyclops and Emma Frost were captured by John Sublime (leader of the U-Men) as he forced Martha the mutant brain to telepathically subdue the X-Men. Both managed to escape, and a freed Martha manipulated Emma Frost into dropping Sublime off of his skyscraper.
Beast finally awoke from his coma to warn his teammates Xavier's mind has been trapped in Nova's dead body. Chinese healer Xorn accepted an invitation to join the X-Men in time for another bout with Cassandra Nova. After wreaking havoc on the Shi'ar Empire, Cassandra Nova fooled the Imperial Guard into attacking the Institute. The X-Men are weakened by nano-sentinels that had been planted by Cassandra Nova, but were cured by Xorn. Jean was able to fragment Xavier's mind with the help of Cerebra, and placed a tiny part in every mutant mind on Earth. As Nova returned to the school and was about to use the mutant locater to eliminate every mutant on Earth, Xavier's mind instead reformed and resumed control of his body. Once again pure psionic energy, Emma Frost tricked Cassandra Nova into entering the body of the synthezoid Imperial Guard member Stuff. Trapped, Cassandra was reeducated and unable to flee. The Imperial Guard noted that 'The Phoenix is coming, and she is terrifying.'
With his secret out, Xavier changed his strategy and created the X-Corporation. With headquarters in many major cities around the globe, the new organization acted in more proactive ways to improve human-mutant relations. Unfortunately, the Paris X-Corp had to stop the menace of an experiment of the Weapon Plus program, with Darkstar dying in the process.
Unrest slowly took over the mansion, when Quentin Quire and his Omega Gang boldly pushed Magneto's policies during "Open Day" as humans visited the Institute. Becoming violent under the influence of the drug Kick, the Omega Gang attacked humans and the intruding X-Men. Sophie Cuckoo, one of Emma's telepathic quintet protégé Stepford Cuckoos, perished using Cerebra to stop the Gang's rampage. The grief of Sophie's sister, Esme Cuckoo, led her to reveal Emma and Scott's psychic affair and shot Frost while she was in her diamond form; splintering her into thousands of pieces. Sage and Bishop's investigation found the culprit, but Esme fled the Institute. Although furious at Emma Frost for becoming close to her husband, Jean displayed vast telekinetic power and reformed Emma's broken body.
Xorn pushed Magneto's theories on his Special Class of young mutants. Disapproving, Xavier confronted him only to discover Xorn was Magneto in disguise. Trapping Wolverine and Jean Grey on the remnants of Asteroid M and incapacitating the other X-Men, he destroyed the Institute and took over Manhattan. Moving closer to the Sun, Wolverine killed Jean so she could unlock the power of Phoenix. Cyclops led a last ditch assault on Magneto and his allies, and Phoenix returned in time to defeat the mad mutant. On several occasions, they noted that something was odd about Magneto, which infuriated him. He made various threats such as ripping out Wolverine's adamantium again as 'proof' that he really was Magneto. Knowing he was defeated, Magneto used his stored energy to give Phoenix a stroke 'on the planetary level'. Wolverine decapitated Magneto in a berserker rage as Jean Grey died in the arms of her husband.
New X-Men:
Cyclops
Phoenix
Wolverine
Beast
Emma Frost
Uncanny X-Men:
Archangel
Wolverine
Nightcrawler
Iceman
Chamber
Stacy X
Supporting Cast:
Professor X
Fantomex
Allied Teams:
X-Treme X-Men
X-Corporation
