Jean Grey transcended the physical plane when she used the totality of her psionic power to pilot a doomed space shuttle containing her and the rest of the X-Men. As she shielded herself and the shuttle from cosmic radiation, her sheer force of will enkindled the manifestation of the near-full capacity of her telepathic and telekinetic abilities. In her supreme exertion, she became pure psionic energy. Resultingly, her essence began to transcend her physical form and the material plane as a whole, causing her body to wither due to the radiation that pummeled it. Unprepared for such a shift in perspective and consciousness and witnessing her body wilt, she let out a reverberating psychic cry. Already familiar with Jean since her prepubescence, her bellow, coupled with her sheer psionic power and purity of heart, soul, and intent, compelled the Phoenix Force to come to her aid, protecting her body and essence from both the ravages of radiation and her own unbridled power. It fashioned a new body for her, placing her old body in a cocoon and fusing her essence with the clone, which the Phoenix Force also inhabited to stabilize and reinforce the binding. Thus, the union between Jean Grey and the Phoenix Force was complete.
However, it was a union the Phoenix Force intended to sustain only through the duration of Jean’s psychic and physical rehabilitation and gradual adjustment to her quickened power advancement. Later, when Mesmero hypnotized her and Mastermind, with the help of the White Queen, penetrated her mind, it was the Phoenix Force that prevented either of their powers from taking complete control of Jean’s psyche. Unfortunately, still reeling from her experience on the shuttle, Jean was further traumatized by the aforementioned psychic violations perpetrated against her and the insidious interruption of her healing. Additionally, incited by Jean’s pain and trauma and the abusive behavior she was subjected to, the Phoenix Force's destructive side, i.e., one aspect of its raison d'ętre – to burn away the defective and obsolete – was initiated. Although Jean fought to repress both, her trauma and the Phoenix Force’s instinctive destructiveness overwhelmed her. Jean's pain soon turned to rage, which merged with the Phoenix Force's wrath, resulting in a primal fury that became addictive in its search for recompense and sanctification.
Later, to protect both her friends and the cosmos at large, Jean killed herself in the Blue Area of the Moon. In that instant, Jean’s mind, heart, and soul synchronized and revolted against both her own trauma-induced rage and addiction and the Phoenix Force’s wrathful reflex to destroy what it deemed flawed and deficient, killing the clone it had created for her. But, recognizing the selfless, courageous, and transcendent nature of what Jean had done for a second time, the Phoenix Force chose to preserve her essence, returning it to her former body, which lay encased in the cocoon it had created at the bottom of Jamaica Bay. Furthermore, the Phoenix Force imparted a fragment of itself to Jean so that she could continue to heal more rapidly than she would on her own. Since then, it has attempted on various occasions to unite with her once more. But Jean, not having fully faced and healed from the trauma she endured either on the shuttle, at the hands of sadists, and when possessed by the Phoenix Force’s darkest facet, has chosen to reject it on most occasions.