The X-Men ran into Jubilee while at the mall. The latter was taken back to the Xavier Mansion and there, tried to escape. Once she made her way through the halls, Jean and Charles walked into the planning room, where Jubilee had been before hearing the two coming and hiding. As Charles expressed dissatisfaction in how the X-Men had been revealed to the public, Jean pointed out that the monitors had been on when the two were in there. Charles realized that she had previously been there and ordered the X-Men to look for her. Jubilee was met by the rest of the team sometime after and captured by a Sentinel afterwards.
Following Scott's proposal and Jean's acceptance of it, Jean and Scott had a Wedding. After being asked by their administrator of marriage if he would take Jean as his wife, Scott confirmed that he would. This was soon followed by Jean taking him as her husband and kissing him upon being allowed to. While the regular conversations commenced, Jean felt a bad vibe from the non-present Wolverine as she was kissed on the cheek by Gambit, who explained that where he was from they always kissed the bride. Despite this odd feeling, Jean portrayed herself accordingly for what was supposed to be one of the best days of her life. She asked the attendants of the wedding if they were ready to throw the bouquet before throwing it, with the pile of flowers landing in the hand of the arriving Beast. Walking down and smiling, Jean told him that if he was going to be the next to marry then perhaps the X-Men should start calling him Mr. McCoy.
Returning to the Xavier Mansion, she found a battle damaged Wolverine in the Danger Room. Wolverine had previously been fighting a visionary version of Cyclops and later, a Sentinel with his head, all the while telling him that he could not have Jean. The latter told him upon arriving that she and the others had missed him at the wedding, causing Logan to tell her that he must have lost track of time. As Jean walked over, Logan told her that he was sorry he could not be there. She soon began walking away, as Wolverine tried to explain himself. Jean told Wolverine that she had to go and explained that she and Scott had a plane to catch.
With the Phoenix still inside of her, Jean underwent treatments by Moira McTaggart, who tried to get her to remember that she had taken the M'Kraan Crystal into the sun and asked her what happened to her inside the sun. Jean began to scream after McTaggart asked her why the Phoenix had not left her alone yet and was soon contacted by Charles, who told her that they were there for her before the Phoenix Force stated through her body that she was as well. Charles asked Phoenix why she remained in her body and stated that she did more harm than good by remaining in her before the Phoenix caused the treatment center to explode. After the explosion, Jean uttered to the non-present Scott to help her. Scott was at a club when he received her cry for help telepathically and returned to the Xavier Mansion after stopping Dazzler from being kidnapped by a few members of the Inner Circle. After Wolverine pointed her out to him, Scott came to Jean and hugged her.
After Scott asked her how she was, Jean told him that the therapy worked and that she was better before Charles ended their reunion by stating that the two could talk after she received some rest. While in the hospital, Charles asked Jean what the Phoenix wanted. Jean replied that the Phoenix hungered and prompted a reply from the Phoenix herself, who confirmed that it did indeed. The Phoenix started to make large bright lights come out of Jean's mouth and eyes, prompting Cyclops to tell Charles to help him before the latter told Jean to control her. After Charles left the room, Scott revealed that he would have to go back to the club he attended the previous night, to ensure that the Inner Circle did not return for Dazzler. With the Phoenix dominant, she told Scott that he could leave her for another woman and stressed that he might have to protect her from him. Scott told her that she did not mean that, prompting Jean to tell him that while she did not, the Phoenix did. Scott assured her that he would stay longer and would find a way to help her.
Later that night, Storm approached Scott as he slept. She told him that it was getting late and that he should go before assuring him that she would watch Jean. Scott thanked her and promised that he would come back. With Scott gone and Jean asleep, Inner Circle resident telepath Emma Frost entered her mind, with Jason Wyngarde using his powers of illusion to create a fantasy. In the fantasy, Jean awoke to nearly-drowning in a sea before being saved by Shaw. He took her back to his ship, where he laid her in bed as she told him that she was not in her proper world. Knowing that she was correct, Wyngarde told her that she needed her rest and shushed her as she tried to explain her position and told her that all was well. Wyngarde fabricated a lie, telling her that she had stowed away on his ship and was desperate to see America. Jean lamented to him that she recalled another life, calling it strange and filled with unusual people that were somehow her friends while obviously referring to the X-Men.
Jason assured her that it was all a dream and asked her if she remembered how frightened she was when he found her. She recalled that he had told her about how beautiful she looked and confirmed that she remembered. After Jason told her that he would always be there when he needed him, the two kissed, with Jean reminiscing about when she married Scott. After waking up, she screamed and was comforted by Storm, who asked her if anything had happened to her. Jean told her that she merely had a dream, before stating that it had felt so real and asking Storm if she could get her a glass of water. While Storm left, Jean flew out the window of her room and after landing, found herself in her Phoenix costume before telling it to stay back and making her way into the club Scott was in. While roaming, she questioned why she was even in there and was devastated by seeing him be kissed by Dazzler. After Jason arrived at the club, Jean walked up to him and morphed back into her clothes in the fantasy and kissed him.
She willingly went with him to his ride and soon arrived at the Inner Circle's base. She and Jason had a wedding ceremony, where she agreed to take him as her husband before Rogue arrived and told her to snap out of her delusion. The X-Men soon arrived after her and fought the Inner Circle for her. Despite their initial disadvantages, the X-Men began to dominate the group before Jean made her willingness to serve them known when she shot Storm in the back. After Storm questioned why she would go against her, the Phoenix confirmed that it was not Jean's doing and that it was only her body before stating that she was Phoenix as her eyes began to glow. With Wyngarde thanking her, the Phoenix went over to him and kissed him.
Following their kiss, Wyngarde redressed the Phoenix in Jean's body as a member of the Inner Circle and took her into the room. After he argued with some of his fellow members of the Inner Circle, Sebastian went up to her and gave her a kiss on the check while asking her if he should refer to her as Jean or Phoenix. Sebastian explained to Cyclops after he yelled out that the X-Men were allowed inside their building so that he could introduce them to the Inner Circle's newest member, as he threw his hand in Jean's direction. Sebastian told her that her power and beauty were all inspiring before asking her if she would freshen up outside as he discussed her with the other members of the Inner Circle, the whole group discussing how they would keep her under wraps and control her power. Jean was brought back in and made to eat with the rest of the Inner Circle. The group toasted in her honor, causing Jean to show visual appreciation before toasting as well.
Cyclops telepathically contacted her, which caused her to show a worried facial expression that Emma Frost quickly picked up on and learned that he had made contact with her, soon allowing Wyngarde back into her mind and starting a duel between him and Cyclops. Jean approached Cyclops during their duel, who told her that he had come to free her. However, Jean claimed that she had already been freed and that she had been set free from the constraints of sympathy and morality that bind ordinary human beings. She told him that the Phoenix Force inside of her hungered for more and that Jason Wyngarde had shown them the way before questioning gleefully if he could see it all around him. As Cyclops told her that Wyngarde was deceiving her, Jean began to laugh menacingly at him and remarked about the dark joy of destruction. Wyngarde striked Scott in the stomach with his sword, seemingly killing him.
After Sebastian questioned if Scott was still alive, Wyngarde confirmed he was not by stating that when the mind perished, there was nothing to control the body and stated that his wife Jean had taught him and demonstrated that as he put his hands around her. However, Cyclops was not deceased, explained by Emma Frost as having still been connected psychically to Jean Grey. After being ordered to finish him off, Jean made her way to him before being completely interrupted by Wolverine. Ordered to stop him, Jean attacked him and nearly knocked him out as he laid defeated. Jean made her way to him and planned to execute Wolverine, before recalling when she came to his aid while he tried training during his injuries from Sabretooth. Regaining her senses, Jean questioned what she had done and questioned what she had let the Phoenix do to Scott.
Wyngarde told her that he had a job for her, to terminate Sebastian Shaw. She began to laugh manically, stating that no one controlled the power of the Phoenix and blindsiding Cyclops after he told her to talk to him while under the impression that Jean had regained full control. The Phoenix stated that she tired of their squabbling and told them to amuse themselves as she departed. While standing atop the roof of the Inner Circle's domain, Jason Wyngarde approached her, with the claim that she had entered her nightmares again and that he had come to save her and take her back to her real life. The Phoenix told him that his pathetic attempt to use her had opened her eyes. As Wyngarde pleaded to be spared of her wrath, Phoenix pinned him against a wall and soon told him that through Jean's body, she had discovered evil and thirst for more. She told him that she was tired of his illusion and allowed the world to see how ugly he was by revealing his true form of an aged man. She then asked him if he would like to see her in her own true form and attacked him with it. Cyclops arrived and cried out for Jean, only to be told by the Phoenix that the mortal Jean Grey was no more and revealed herself as the Dark Phoenix, much to Cyclops's dissatisfaction.
As the X-Men plead with her, she asked them if they wished her to return to the nothingness of space and if they wanted her to give up the body before she refused without answer. She told them that there was a power, beyond good and evil. She revealed it to be the power of creation and destruction as she held a flame in the shape of a horse and crushed it with her bare hands. Cyclops called out and asked if Jean could hear her. The Phoenix told him that Jean Grey could not hear anything and stated that he could only speak to the Phoenix. Cyclops reused, and told Jean to use the powers of her mind to fight the control before telling her not to leave him. Regaining control, Jean spoke to him briefly, telling him to help her before the Phoenix returned. After tossing the X-Men aside, the Phoenix went to the group and told them that they were at their ends, announcing her plans to terminate them.
As the X-Men attacked her, she began to gloat and asked them if they really thought their puny powers had any affect on her. As Cyclops shot at her chest while requesting that Jean forgive, the Phoenix claimed that it was all to easy to fight the X-Men and that they merely provided her with annoyance. The Phoenix shot down Storm with her own attack and easily disposed of Rogue and Wolverine while questioning why her then-recent sensation lessened when the opponent was weak. Taking Gambit out, Beast jumped on her and tried to hold her down for Cyclops to shot before being blasted himself instead of her. After Rogue tried to absorb some of her powers, Phoenix ordered her to stop it as she tossed her aside and questioned if this was all they could do against her and claimed that it was too easy before Cyclops blasted her again while telling her to give Jean back.
The Phoenix asked him why he cared so much about the person she was using before Cyclops told her that he loved Jean, something she stated that she could not understand and told him that his answer was unacceptable before shooting him in the chest. After Cyclops went down, Jean returned again and told him that she would always love him as she put his visor back on him. The Phoenix flew into the sky and then into space, and plunged into the sun as the Shi'ar watched her. Despite their initial belief that she had killed herself, it turned out that the Phoenix was actually feeding on the sun. The Phoenix then destroyed an entire star system, prompting the Shi'ar to want to destroy her as well. Jean returned to the home of her parents, reuniting with her cat Prometheus and hold an old bear of hers while beginning to sob. Seeing a car pull up to her home, she believed it to be her returning father and went out to see him before Gambit placed a Brain Buster atop her head and the Phoenix regained control.
As Storm tried to convince Jean to allow her friends to help her, the Phoenix told her that she had no friends and shot her away. The Phoenix override the circuitry as Wolverine tackled her and prepared to finish her off. After Jean regained control, she told Wolverine to finish her off while she still had control. Though Wolverine stressed that he could not, Jean told him that if he truly loved her he would do it before the Phoenix returned and told him that he should have destroyed her when he had the chance. Knocking Wolverine away, she melted the Brain Buster and told Beast that she had ruined his little toy. Lifting the X-Men into the air, she told them that they would now play on her terms. Cyclops arrived and told Jean to let them go, with Phoenix responding that Jean Grey no longer existed. As Cyclops told her that she could not destroy her friends and Jean regained control, Charles attacked her from the mind.
Despite briefly knocking her out, Jean soon regained her consciousness as the Phoenix and pushed the X-Men away before telling Charles to enjoy the fact that his pupil had surpassed him. Charles entered her mind and had a battle against her. Despite the Phoenix insisting that she had the superior powers of the two, Charles was able to constrain her in Jean's mind with help from Jean herself. After awakening in the arms of Cyclops following the mind battle, Jean and Cyclops briefly exchanged teases before the Shi'ar arrived, with the intentions of ending Jean Grey and the Phoenix.
Death and resurrection
The only way to save Jean Grey's life, as Charles Xavier put it, was to duel the Shi'ar in their names for honor. The X-Men were teleported above their ship, where Cyclops talked to Rogue about having to be in Lilandra's position and his belief that he would spare Jean if he was in such a ranking. Jean reappeared to him, noted by Cyclops as wearing her old uniform and stating that it was the one she was wearing when she first got to know him. After Rogue left, Cyclops tried to talk to her before she shushed him and lamented that she had destroyed a solar system. Though Cyclops tried to continue to defend her against herself, Jean gave him a mental viewing of her activities as Phoenix and stated that before he said more, he would need to see what she had done.
Jean stated that she could lose control again, except this time her victims would be her friends and the world that she called home. Jean asked Cyclops if she was worth the risk, prompting Cyclops to tell her that she was worth everything there is. While being hugged and comforted by him, Jean told Cyclops that she loved him as well and said that her love was with all her heart as the two kissed. Lilandra had the X-Men duel the Imperial Guard. Jean and the rest of the X-Men arrived on the moon, which was depicted with several ruins and detail instead of its more recent appearance. Jean told the X-Men that she was picking up multiple telepathic impressions. Being attacked by the Imperial Guard, Jean primarily partnered with Cyclops as they engaged them. While fighting the Imperial Guard, Jean stressed to Cyclops that she had lost telepathic connection with the other X-Men and that she thought they were the only ones left. Suggesting a different path, Jean took Cyclops with her to a secluded space. Though Cyclops told her that they would be spotted easily, Jean covered the two from their enemies. Cyclops told her that they did not have much time and expressed the many things that he wanted to with her that he had not been able to, prompting Jean to tell him that thought counted the most where she was from and that his were beautiful like he was. The two kissed and held hands, before Jean asked if he was ready as Cyclops took her hand as the two charged against the rest of the Imperial Guard. Despite their splendid mixing of their abilities, Cyclops was struck during their attacks. After he fell, Jean came to his aid, removing a large substance that was on top of him. After Cyclops told her that he had let her down, Jean was taken over by the Phoenix Force.
Immediately dominating the Imperial Guard, Phoenix told Gladiator that she had missed tossing him around before doing so. Charles Xavier had signaled the X-Men and told them to strike Jean, including Cyclops. Wolverine could not bring himself to kill her, something Phoenix regarded as touching before taking him out. After Rogue and Beast struck her, Cyclops buried her underneath the ruins while apologizing to Jean. Jean regained control and got herself from underneath the ruins, before asking Cyclops to help her. Jean requested that he end her, as she did not want to go everyday of her life struggling to keep control within herself and never being able to slip. Since Cyclops would not kill her, Jean took to running away from him and into the beam of Lilandra's ship, which she fired at her.
Being presumed dead by everyone, the Phoenix revealed it had lived and reviewed it's past with Jean, before stating that it had gained emotions through her and acknowledged that she had lost her way. Phoenix told them that since the fire in Jean Grey had been extinguished, she had now returned to her previous state. Cyclops asked the Phoenix about Jean, before being told by her that the flame in Jean was no more and it could only be rekindled by taking it from another. Though Cyclops and Wolverine argued over giving their own lives for her, the Phoenix offered the alternative of small portions from many sufficing for the restoration of her life. The X-Men agreed and all gave pieces of their lives to bring her back. With life returned to her, Jean and Cyclops expressed their love for each other before being returned to the Xavier Mansion. While laying in bed, she was tucked in by Cyclops and kissed on the forehead as he stood by her bedside.