On the nameless planet that is home to the M’kraan Crystal the X-Men and Starjammers stand above the scattered, unconscious bodies of the Imperial Guard following their battle. The M’Kraan Crystal itself is going crazy unleashing vast amounts of energy and neither team is sure what is going on. Corsair tells Ch’od to call Waldo –the ship’s computer – and to tell him to do a full range sensor-scan to discover what is happening to the Crystal. Wolverine suggests they find a way to get home, this place is giving him the creeps. But Lilandra tells him that they couldn’t hide even there from a force known as ‘The End of all that is’. Hepzibah, always jumping for a chance to take a dig at Lilandra, scornfully tells her that while they live, they fight, but Nightcrawler is quick to point out that there is nothing to fight.
Banshee demands an explanation from Cyclops who recalls about how Phoenix took them through a star-gate to the M’Kraan world after Professor X sent them to save Lilandra who had been kidnapped by Erik the Red. There Lilandra’s brother D’Ken was trying to access the power absolute of the M’Kraan Crystal. In order to stop him the X-Men were thrown into battle against the Imperial Guard, the battle seemed lost until the timely arrival of the Starjammers turned the tide of battle in their favour. It was then that nine mystic death-stars aligned, their light fell on the M’Kraan Crystal and all of reality went ‘Blink’.
Back above Earth aboard the Starcore satellite, Peter Corbeau is holding a conference with the President, The Avengers and The Fantastic Four via satellite about the ‘cosmic blink’s’. The President tells Corbeau that his science advisors question the accuracy of his data that for a fraction of a second, the whole universe ceased to exist. Corbeau however is certain, and informs the others that there is nothing they can do and if it happens again it could well mean the end of the universe as we know it.
The Wasp of the Avengers is angry and frustrated that they can do nothing but sit back and watch the universe die but Yellowjacket tells her that this battle is too big and too far away for them to fight.
Back in space: The X-Men are interrupted by a small purple cute-looking alien calling himself Jahf, a guardian of the M’Kraan Crystal who tells them that no one may approach the Crystal and live. Wolverine takes up the challenge and is instantly knocked outside the planet’s orbit by one punch. Luckily Waldo in the Starjammer is able to retrieve him before he freezes.
Despite the X-Men’s and Starjammers’ best efforts Jahf is able to laugh them all off. Ch’od tries to explain to the guardian that they mean no harm and will leave if they are allowed. Jahf senses the truth in his words but says that will not save them because his programming allows no exceptions. They are here and must therefore pay the final price. Phoenix even telekinetically brings down a meteor on Jahf’s head and still the alien suffers no injury.
Suddenly Banshee comes up with a plan, after realising that Jahf mentioned his programming he guesses that he is some sort of robot and that his sonic scream will scramble his circuits. He grabs Jahf and although the guardian is causing Banshee unbearable pain, he succeeds in unleashing a strong, thin beamed sonic scream and defeats Jahf.
Before the X-Men can take a breather however they are attacked by another giant guardian. He introduces himself as Modt and states that his power is thousand times greater than Jahf’s and that if he should be defeated they will face a guardian whose power is a thousand times greater than his.
While the X-Men and the Starjammers attack the guardian D’Ken watches and gloats about how he will not only gain power absolute but he will also witness the deaths of the Starjammers, seemingly not realising that the guardian will slay him too.
It is then Raza is contacted by Waldo aboard the Starjammer who tells him that when the second guardian appeared there was another cosmic ‘blink’ and whatever the Emperor unleashed is disrupting the basic fabric of the universe! This sends Raza over the edge who charges at D’Ken, picks him up and throws him at the face of the Crystal. Suddenly everyone present is caught in a blinding flash of light and find themselves transported to some sort of silent city.
Storm states that although she has never seen such emptiness she feels trapped. It is only Phoenix who understands and who tells the others that they are inside the Crystal, and that is why the guardian is no longer there, he has no power over those who pass him.
In the middle of the city there is a sphere and Jean tells Scott that she feels life within it, and pain, calling out to her. She touches the sphere and then Ch’od points out that her hand has suddenly become transparent. Before Jean can do anything, everyone present is suddenly zapped by beams of light from the sphere which plunge them all into their deepest personal nightmares. For D’Ken it is facing his pet, the Soul Drinker, knowing that it has come after him. For Nightcrawler it is being hunted, caught and killed by a mob made up of his dearest friends the X-Men. For Corsair it’s the memory of having his wife Kate killed by D’Ken.
Phoenix’s nightmare is death, however there is a sense of déjà vu because several months ago while Jean Grey piloted a space shuttle through a solar storm she died due to the solar radiation, and was reborn as Phoenix. Suddenly she realises that the nightmare is no longer having an effect on her because when she died her fear of death died with her. Next to her Cyclops eye beams are going wild because with his mind trapped in the nightmare he isn’t holding himself back anymore. Phoenix attempts to stop him but he sends a beam straight in her direction. Instead of cutting her in half as it should have however it passes harmlessly through her as even more of Phoenix’s body becomes ephemeral. After knocking Scott out with her telekinesis she realizes that it is too late because one blast had already hit the sphere and it is now cracking and whatever is locked inside is breaking free.
Jean tells herself not to panic. She senses that she and the sphere are bound together and while it loses its hold on reality she loses hers. The reason must be inside. As Phoenix enters the sphere, the nightmare field lets go of the other X-Men. While she is in the sphere Phoenix has changed, she is now no longer Jean Grey, she is a giant bird of flames. She feels more alive than ever.
She senses great power there, bound within a live lattice of anti-energy. She also senses that it is dying and when it dies the neutron galaxy within it will be free and as it’s power spreads around the universe it will destroy everything in the process. Eventually reality itself will tear itself apart and give birth to a new virgin universe.
Phoenix senses that she needs to knit the lattice back together, she thinks she knows how to do it but she doesn’t have the power as the Phoenix is a being of energy and the Neutron Galaxy absorbs that energy. Suddenly Storm comes up behind her and offers herself as an anchor in the human plane of reality. Jean realizes that this will work but tells Storm that the anchor she is offering is her life-force, Storm merely tells her that it is her life to give. Phoenix then realizes that if she took two life forces it could leave both donors alive. She calls over to Corsair. When he hesitates, she uses his real name, Major Summers and then takes his hand. It only takes her a moment to take what she needs and as she enters the sphere she tells Corsair to look after Cyclops for her, because he is his first-born son.
At the heart of the sphere Phoenix once again changes into bird form and using amazing amounts of power, reality twists and reforms around her. Panic seizes her as she realises she cannot do it alone, but she then sense the spirits of the X-Men with her. In that instant she succeeds in re-energizing the lattice and she sees that each X-Man has a place and a purpose greater than him or herself. A new pattern emerges, shaped like the mystic tree of life and at the heart is Phoenix, Tiphareth, the vision of the harmony of things. With that she falls unconscious.
Back on Earth, the star-gate energizes once more on the roof of Jean Grey’s flat in Greenwich village, as the X-Men return home. There they come face to face with Firelord. He tells them not to worry however because while they were away Xavier explained to him how he was deceived by Erik the Red and he stayed around to guard the star-gate. Before anyone can respond the star-gate opens a second time and Lilandra emerges through it. The star-gate then melts behind her. Lilandra explains that what happened within the M’Kraan Crystal drove her brother into a catatonic state, by Shi’ar law Lilandra now should succeed him as Empress, but because she led a rebellion she is considered a traitor. But because the council now knows what she did was right when they iron out a few legal problems they will summon her back, but until then she is exiled on Earth with Xavier