After Xorn killed Jean Grey, the X-Men quickly fell apart. Professor X decided that he was finally finished working at the Xavier Institute. Cyclops lost the will to continue trying, and without Cyclops involvement Emma Frost also withdrew. Beast attempted to keep the school going, but quickly burned himself out from the effort. He turned to the mutant-enhancing drug Kick before it was known that Kick was actually the aerosol form of the Sublime bacteria. Sublime took over Beast's body, and used it to continue his quest for mutant extermination. The Sublime Beast would experiment on himself, turning white and slowing down the aging process. With access to genetic samples of all the X-Men he created a hybrid race from mutant DNA that were called the crawlers. The crawlers were based on Nightcrawler's DNA, giving them a similar appearance and his power of teleportation. He continued to develop them, adding in the genetic traits of other mutants and giving the ability to duplicate themselves (from the Madrox), eye-beams (presumably from Cyclops's power), wings, and more. He developed a laboratory that worked as a factory for generating crawlers, and doing other experiments. At some point he gained control of Fantomex, grafting new parts onto him and turning him into the last of his U-Men. Now called Apollyon the Destroyer, Fantomex became the Beast's herald, carrying out his bidding.
Around 150 years from Jean's death a Phoenix Force egg was found dormant on the moon. This was brought to the Earth. The mutants that discovered the Egg did not have it for long as Apollyon was sent to retrieve it for his master. If Beast were to gain control of the egg he would have control over the Phoenix would be virtually unstoppable. The egg was entrusted into the care of Tom Skylark. Tom's longtime companion Rover, one of the last of the original Sentinels, was used to transport the egg. Tom and Rover escaped with the egg as his teammates were being slain by Apollyon and the crawlers. Tom sought out the X-Men to help protect the egg. After he had Rover destroy a pack of crawlers that were following them Tom located E.V.A. E.V.A. was Apollyon's sentinel external nervous system when he was still Fantomex. She took them back to the X-Men's base not knowing that one of the crawlers had hitched a ride inside of Rover.
Back at the X-Men's base the crawler teleported out and began to duplicate himself. E.V.A. called upon the X-Men to help protect the egg. Tito arrived to help beat off the intruders, but several swarmed over Rover and were able to teleport the egg back to the Beast's lair. The surviving three Stepford Cuckoos, now simply going by the three-in-one told Wolverine and Cassandra Nova (now going by Cassandra Nova Xavier) about their dreams of the start of a new dark age. Now possessing the Phoenix egg the Beast would try to live out his dreams of stopping evolution. He could potentially encode the traits of the Phoenix into his armies or even in himself. Tom got Rover back, disinfected and safe. Rover looked even more torn up than before.
Back at the Beast's layer Apollyon begged him for grafts from the phoenix. Beast called upon his crawlers to use their power to incubate the phoenix egg, causing it to hatch prematurely. Jean Grey came out of the egg, drawn back from the White Hot Room early and because of this was confused. Beast greeted her, unknowing that her old friend was now taken over by the Sublime entity. Beast sent her out to kill the Termids, a race of insects, where she found Bumbleboy the X-Men's ambassador to the Termid multitude. She killed him but before sending his consciousness to the White Hot Room she kept his essence in his skull to learn about the X-Men.
Meanwhile Beast had grafted the traits of a mind parasite onto one of his crawlers and sent it to destroy the X-Men. The crawler burst both of its lungs to teleport into the school through the X-Men's shields. The X-Men fought it, not realizing that the mind-parisite was taking hold of them. The out of control X-Men came after the Stepford Cukoos who were held up with Cerebra. Not wishing to be eaten by the Mind Parasite that had taken hold of the others, the Cuckoos turned on an auto-destruct sequence for their consciousness, and slapped each other a high-five as the former X-Men broke into the building.
Deep in the ocean Mer-Max was being attacked by a ship full of Crawlers. Cassandra Nova and Martha Johansson arrived in their jet just in time, sending the Crawlers into fits of pain with intense telepathic noise. Rover, Tom Skylark, Beak, and E.V.A followed right behind. Tom was about to tell E.V.A. something in case they didn't make it, but before he got the chance the Crawlers began to teleport around Rover, and attacked him until he plunged into the ocean depths. Tom cried out for his partner to no avail, and the ocean liner they were on was now sinking.
When Phoenix arrived back she asked Submlime about the X-Men. He told her that they were enemies that needed to be destroyed. He explained to her that they just continue to become more powerful, resisting his influence and dominating the planet. He wishes to finally exterminate them. Sublime sent Phoenix after the remaining X-Men, and he remained at his hide-out. Sublime told the agonized Apollyon about his life which began eons ago. He described how as a bacterial life form he arose from the Earth to become the dominant life-form. Even the rise of humanity could not sway him, and he continued to infect and spread as he pleased. The rise of mutants created generations of homo-superior that were growing more and more immune, some capable of power on a cosmic scale. These mutants challanged his position as the dominant life form on Earth, and for the first time he felt the fear of extinction. In almost unbearable anguish Apollyon demanded Sublime give him the power of the Phoenix, grafts that would finally make him feel whole. As Sublime finished his story he climbed into a chamber which would give him a portion of the Phoenix power, not Apollyon.
Back in the ocean Phoenix had found Wolverine. Phoenix told him how the mutants time was over and that she would be their destroyer. Wolverine tried to talk Jean out of it, trying to force her to remember her life before. Cassandra and Martha flew in. Cassandra had read the Shi'ar files on the Phoenix, and discovered how to telepathically unplug that power from its host. Wolverine caught Jean and she seemed to be remembering her old life. Wolverine described how after her death Cyclops simply gave up, and that Beast eventually became infected by Sublime due to the pressures of trying to run the school. Sublime arrived with his new power and blew up Cassandra and Martha's ship. Beak was the first to attack and was fried by Sublime. Tom summoned what he could of his power to call Rover back to help. Sublime fought off both Rover and E.V.A., causing E.V.A.'s software to go haywire. After watching Beak die Wolverine lunged at Sublime, but it was no use. Sublime turned off Wolverine's healing factor and cast him aside. As he fell Martha assured him that they were all going to the White Hot Room.
As Sublime believed his victory was guaranteed Phoenix informed him that he had lost. She extracted the Sublime bacteria from Beast's body. Beast was back, but not for long. Appolyon had arrived and removed Beast's head. Wolverine was finally at peace and Tom rushed to aid the dying E.V.A.
Phoenix went back to the White Hot Room where she sanitizes that timeline by cutting it off where it went bad. Hundreds of other Phoenix hosts were there with her and helped her including Kid Omega, the Green Phoenix. Here Jean was dressed in a white and gold Phoenix outfit as the White Phoenix of the Crown. She healed the broken time-line, urging Cyclops to live. Back in the present, when Scott had made the decision to abandon the X-Men (thereby causing this timeline to occur) Scott was again presented with the decision to leave or stay by Emma Frost. Standing over Jean's grave Scott decided this time that he wanted to go on, fixing the time-line permanently.
Planet X - Jean's death at the hands of Xorn created the alternate time-line where Here Comes Tomorrow takes place.
This reality is designated Earth-15104.