The story begins with a sudden explosion at the Xavier mansion which was initially perceived among the X-men to be an attempted attack by an unknown assailant, targeted at telepaths, particularly involving Professor Ch...展开arles Xavier and Jean Grey, who consequently go missing in the immediate aftermath. The resulting trauma caused the X-Men team to disband and go their separate ways, leaving Xavier's once highly revered league of mutant peace preservers out of commission. Due to the heavy losses of the Professor, Jean, and the Mansion, many of the X-Men have withered in their faith towards the stability of their former team and have since detached themselves from their former community. Some examples include Cyclops' depression and subsequent isolation resulted from Jean's disappearance, Storm's relocation back to her home continent of Africa, and Iceman's move back into his parents' home in the quiet suburbs. One year later, the MRD (Mutant Response Division), a government-supported organization created for the detainment and subsequent registration of existing mutants, begins capturing mutants from all over the country in response to the countless human protesters determined to protect the safety of humankind. This course of action causes Wolverine and Beast to ally and resolve to bring the once defunct X-Men team back together again. Thanks to the generosity, wealth, and resourcefulness of Angel, the slowly reforming X-Men team begins to see a promising return to its former glory with the rejoining of junior members Iceman, Shadowcat and Forge along with the reconstruction of the previously demolished Xavier Institute. Unfortunately, without the necessary capabilities of a competant telepath to operate Cerebro, the possibility of locating some of the more globally-scattered X-Men members along with the missing Xavier and Jean seems all but a distant dream.
Fortunately, this problem does not last for very long when Emma Frost, the former Headmistress of a now inactive mutant school of her own in Massachusetts, makes a surprising appearance on the doorstep of the Mansion with an interesting proposal: membership with the X-Men in exchange for the promise of utilizing her telepathy to pinpoint the missing Xavier's whereabouts. Upon the team's and particularly Wolverine's reluctant acceptance of the offer, Emma's efforts prove successful as she is able to locate a comatose Charles on the shores of Genosha in the care of Magneto. After their arrival on Genosha and a short confrontation with the master of magnetism himself, Magneto eventually permits the X-Men to take his old friend's body back to the sanctity of the Mansion where he is certain that Xavier will be placed in proper care. Upon their return, Xavier telepathically contacts the X-Men twenty years from the present in an alternate dystopian future and informs Wolverine that he is to lead and reunite the X-Men if they wish to successfully prevent the inevitable war that will cause the world to fall under the domination of Master Mold and the Sentinels.
Throughout the course of the entire season, Emma's role as the X-Men's primary acting telepath enables the team to relocate the rest of the other members in the hopes of reforming once again and assisting in Xavier's cause. While some were met with initial hesitancy such as with Nightcrawler, others such as Storm were more than willing to accept the offer once Xavier's vision had been put into perspective. The X-Men overcome many hardships and obstacles along the way upon achieveing their ultimate goal of relocating Jean and finally revealing the truth surrounding the mystery of the Mansion's cause for explosion along with Xavier and Jean's subsequent disappearances.
It is later revealed in the 3-part season finale that the previously assumed attack on the Mansion was not from the efforts of a third party, but rather from the result of Jean who unwittingly releases the highly destructive power of the Phoenix Force, that originally lay dormant within her subconscious, in an attempt to halt an oncoming psychic attack lead by Emma - who was secretly working as a double agent for the Inner Circle - and the Stepford Cuckoos.
Along with Sebastian Shaw, Selene, Harry Leland, and Donald Pierce, it was the Inner Circle's utmost duty to not only obtain the power of the Phoenix Force by abducting Jean from the protection of Xavier and the Mansion, but to also obliterate the ancient being's existence before it could fully mature and consequently bring forth unparalleled destruction onto the world as it had done numerous times in the past throughout Earth's history. However in a move that was completely unknown to Emma at the time, the rest of the Inner Circle members all shared an entirely different and more sinister vision than Frost had initially believed: to control and manipulate the power of the Phoenix Force and have it cater to their own hidden agenda. Upon realizing the error of her ways, Emma betrays the Inner Circle and attempts to redeem herself in the eyes of the X-Men by not only rescuing Jean but by also following through with her original plan of destroying the cosmic entity before it could mature.