Beast started preparing a machine to contain the Phoenix Force as Cyclops prepared himself in the Danger Room to kill his wife. Quentin (Kid Omega) decided on using the Phoenix's help to revive the deceased Cuckoo and so seeks her out. Problems arrose when the Shi'ar discovered that they had not, in fact, destroyed the Phoenix Force (their earlier attacks had only managed to weaken it), and continue in their pursuit.
Storm and Nightcrawler went to stop them since they had to contain the Phoenix before it inevitably killed again in the machine Beast had created. Using Cerebra, Emma located Jean and the X-Men (Cyclops, Emma Frost, Beast, Angel and Kitty Pryde) took the fight to her. Colossus stayed behind on Cyclops' terms saying that they couldn't have him pull his punches like before. Kitty and Peter said their good byes. Meanwhile, Jean had suceeded in separating herself from the Phoenix force and buried herself in ice, leaving the Phoenix to roam without a host in the form of Jean Grey. Arriving there Kitty uncovered that Jean was under the ice - but that's when the Phoenix attacked. Quentin Quire was getting closer to his goal but the corpse's hand kept falling which stopped him along the way. The Phoenix then revealed the true nature of her return, she wanted a power supply for herself and the beams in Scott's eyes were what she needed. The X-Men and the Phoenix force went on in an epic battle while Storm and Nightcrawler were trying to stop the Shi'ar agents. Scott came up with the plan of having Kitty kill him by crushing his heart, but the Phoenix kept talking of how much she loved Scott. His heart jumped by hearing this and asked Kitty to kill him. Emma stopped her by stepping into the rogue force's path and that's when Scott's heart truly jumped of joy. Emma reassured the Phoenix that she kept talking about love for Scott because she remembered what Jean wanted, but her emotions were merely an echo of Jean's. Emma then offered herself as a host of the Phoenix force. Kitty, who worried what this power could do to the former "White Queen", phased through Emma's body and put her hand around her heart. Scott told her to allow the Phoenix to take over Emma.
Emma, now struggling to control the power of the Phoenic Force was pushed by Scott inside the egg shaped machine Beast had created. The Phoenix and the beams from Scott's eyes had found their destiny, they were in equilibrium, but Scott and Emma were now stuck in there indefinately. Kid Omega liberated them both and the Phoenix granted Quentin's wish and revived the Stepford sister.However, Sophie refused Kid Omega and fell dead again. Jean Grey then came out of the ice and went against the force and pulled it out of Emma. They both bonded again in good terms allowing her to have control. Using Cerebra the Stepford Cuckoos showed Jean all the people that loved her and the people who miss her. The Shi'ar agents then attacked but Jean protected her fellow X-Men. In the end Jean took Scott into the White Hot Room, revealing herself to be the White Phoenix of the Crown - the most powerful incarnation of the Phoenix where host and force are utterly combined . As a last request she asked Scott to let her see his eyes and then said good bye.
The Stepford Cuckoos then were seen waking to the Phoenix's force in their minds.
Note: The events of what happen later with the Stepford Cukoos happen in Phoenix: Warsong.