In Space, the shuttle housing the X-Men is still plummeting towards Earth. In the cockpit, Jean is knocked out of her seat by the turbulence. She is struggling to maintain the telekinetic shield which protects her and still pilot the ship at the same time. Finally, her shield fails, and the radiation begins to attack her. Just then, a strange bird-like entity seemingly composed of fire flies through the cockpit and into Jean’s body. Instantly, she wakes up, and re-erects the shield around herself. Only this time, her power manifests itself as fiery red and not her usual blue.

She flies the ship safely into Earth’s atmosphere, and it crashes into the New York harbour. As it does, it splits apart, and the radiation chamber in which the other X-Men were housed floats out. As water starts leaking through, Cyclops blasts open the hatch. They swim to safety. However, once they reach the surface, Cyclops notes that he can’t find Jean. He and Wolverine are still looking for her, when a patch of water starts to boil nearby.

Eventually they notice it, and watch in awe as Jean flies out of the water dressed in strange new attire. As she flies higher and higher, she says regally: “I AM PHOENIX” Upon saying this she collapses and the X-Men move in to save her. In the next scene, the X-Men watch how harbour patrol extracts pieces of the shuttle from the harbour. Cyclops explains to Jean what happened and Jean states that she does not remember, and asks how she survived. Looking away, she asks ‘if’ she survived. When the X-Men tell her that she did, she states that she feels strange. As if she could reach out and touch the moon and crush it in her hand.

Then, Cyclops asks her who Phoenix is, and Jean’s eyes begin to glow. She asks whether or not she is Phoenix. Just then, the Professor and Beast walk in. While the Professor speaks to Jean, Beast pulls Cyclops aside, and explains that NASA cannot account for the Space Ship that came through the vortex, or for that matter how the X-Men survived. Just then, Professor Xavier enters the room. Cyclops states angrily that it’s time the Professor told them everything he knows about the situation. The Professor defends himself saying that he has told them all that makes any sense. Cyclops, now yelling, says that that is not good enough. The two of them continue to exchange strong remarks until Beast states that both of them have rendered irrational out of concern for Jean’s condition. He leaves the Hospital and finds Wolverine tossing trash cans around. He asks why Wolverine doesn’t go in to see Jean. And Wolverine states that he doesn’t like Hospitals and pops his claws bitterly.

The Professor goes to the roof and gets into a mini-jet. Just then, his mind is once again filled with strange images, primary among them is the image of a crystal, and a person dressed in armour reaching out to him. Finally, the vision ends and he collapses. Just then, a ghostly image of himself steps out of him and levitates next to the jet. He searches telepathically for the X-Men and then disappears.
On the Subway, Wolverine stands steeped in thought. Suddenly, he sees his former lover Yuriko, standing in the next car. He chases after her but she is gone. In her stead, he finds Sabretooth, who engages him in battle, when Wolverine attempts to fight back, he disappears. Now behind him, there stands Omega Red, he walks toward Wolverine and changes first into Maverick and then into Deadpool, who fires a gun at him. Wolverine grabs onto the edges of the doorway with his claws. Then, the image Deadpool changes into the image of the Professor, the same one who stepped out of the unconscious body of the real Professor X.

This ‘Professor’ blasts Wolverine onto the tracks with an energy blast. He levitates in front of him, and calls Wolverine an animal. He tells him how sick he is of his constant arrogance and defiance. As Wolverine moves to attack the Professor, he hears ‘Jubilee’ scream behind him. She has been tied up, and is now lying on the tracks. The Professor manifests a gun in his hands, and fires sticky goo at Wolverine’s feet, immobilising him. He claws at it and gets free. As he picks up ‘Jubilee’ she disappears. He narrowly makes it as he dives out from in front of an onrushing train.

On the street just above him, Gambit and the real Jubilee stand in line for tickets to a Broadway show. Just then the ‘Professor’ appears behind hem, he blasts Gambit away, and blasts Jubilee into the middle of the street. Wolverine is able to rescue from being hit by a car. She asks about Professor Xavier walking, and Wolverine states that the person they see is not Xavier. Gambit extracts a card and charges it, but the ‘Professor’ seemingly manipulates the card telekinetically and causes it to explode inside the ticket office. As he blasts Gambit again, Jubilee tries to take out the ‘Professor’ with a blast of pyrotechnics. He disappears, but reappears above them, stating their powers can’t hurt him.

Atop Brooklyn Bridge, Storm sits meditating, when her communicator goes off. It’s Jubilee, She calls Storm to Time Square as the Professor has gone “nuts”. She flies off, and the Professor, who apparently can telepathically see everything, that is happening says that Storm shouldn’t go, as ‘he’ will only hurt her too. Back at Time Square, the Police show up and threaten to arrest the X-Men. When Jubilee points to the ‘Professor’ and says that they should arrest him, they don’t know what she’s talking about, as there is no one there.

Wolverine realises that there is no one there as he can’t smell him. Just then, the ‘Professor’ disappears. Wolverine intends to fight the Police, when Storm shows up, and cloaks the entire neighbourhood in fog. Allowing them to escape safely. In Jean’s Hospital room, Cyclops is on the hone to Rogue, who is still on her undisclosed mission. Suddenly, the ‘Professor’ appears in the door and fires a blast of energy at him. Cyclops is pinned against the wall. He fires an optic blast at him, but it goes right through him. The ‘Professor’ fires another blast at Cyclops and he is once again pinned against the wall. Just then, Jean wakes up; she tells Scott that it is all in his mind and that there is no force beam affecting him. Then, a tiny bird of fire appears around her head and she fires a bolt of energy at the ‘Professor’ and he is destroyed. She telepathically contacts the Professor whose mind she states is out of control.

On the roof, the X-Men stand around the mini-jet. As Professor Xavier explains that the circuit breakers he placed within his mind to control his dark-side were ripped away by a probe of immense power. He states that his orders can’t be trusted and that he is going away. Unbeknownst to them, they are being watched by one of Eric the Red’s emissaries from the shuttle, still under mind control, he stands looking at a screen and says that Xavier is the key. The next day the Professor arrives on Muir Island. Where he is met by Moira Mactaggert and Sean Cassidy, whom she reveals, is her fiancé. Irritated, he asks to be shown to his quarters.

That night, he sits at the window, trying to telepathically locate the person who has been contacting him. Outside, Moira and Sean are talking, they start to kiss and don’t notice when a beam of energy in sent into Charles’ room. Inside, he hovers above his wheelchair, and states that though this person is driving him insane. He will not resist. Again the person reaches out to him, this time he takes her hand, and the vision ends.

When he opens his eyes, there is a person standing in front of him dressed in otherworldly armour. She collapses at his feet and he asks her who she is. She removes her mask and introduces herself as Lilandra. Rather than hair, she has feathers sprouting from her head, and also, she has strange tattoos around her eyes. She explains that she comes from a world called Shi’ar and that she needs his help. He asks her why, in response, she places her hand on her temple and displays her own telepathic powers. Filling his mind with images.

She explains that she is the sister of the Emperor and that she served him loyally once. Until she learned of his ambition to harness the power of the ancient crystal of M’Kraan. Revealed to be the crystal in his hallucinations, Lilandra states that it is the most dangerous source of power in the universe. And that if her brother succeeds, both of their universes would be at risk. She explains that she stole the crystal and that this is why her brother tried to destroy her and her ship.

The Professor then asks why she chose him. She explains that her people believe that two people can be joined from the moment of their creation by a bond much stronger and deeper than love. She asks if he also believes this and he says that he does. She touches his cheek and states that she has seen his face a thousand times within her mind.

Just then, there is a ring at the door, Xavier mistakenly thinks it is Moira Mactaggert and tells her that it is all right, but then The Juggernaut bursts through the door and grabs Lilandra.