This is what I've got so far in terms of a general plot treatment. But it's become a little convoluted since I've been trying to incorporate others ideas that I liked into it. Some of the scenes probably aren't in the best of order.
MAGNETO VOICEOVER
There is only one constant in the universe and that is change. Evolution is change, the process by which novel traits and species emerge from their predecessors. Often evolution requires destruction; war has always been the greatest mother of invention. The strongest steel must be forged through fire and thus evolution deems that only the strong rise from the ashes of the past… like a phoenix reborn.
EXT. ALKALI LAKE, CANADA
The waters have receded. A red-haired woman lies naked on her side in a foetal position. Her face is unclear but her identity is not. Zoom into her skull through layers of flesh and bone to a lifeless neuron. A spark of orange fire lights up the neuron and this fire travels through the brain and down a nerve to a lifeless heart. When it hits the sinoatrial node a wave of fiery orange electrical activity spreads through the heart and it beats. The camera enters the heart and follows red blood cells as they begin to pump around the body. The fire follows too, as the blood is pumped to an ocular artery. Zoom out from the blood stream through fluids, the lens and the eyelid to a close-up of the closed eye. It opens filled with flames. Fire spreads from her body in all directions along the ground melting ice, burning trees instantly to cinder and scorching the earth. Zoom into the iris/pupil as the doors to Cerebro close around it. Zoom in on the ocular scanner.
We are shown that Jean had enormous potential but little control as a child. Show how Jean's powers first emerged, the car accident when she was about 10 or so. Her friend, Annie Richardson, is dying in her arms and she can feel the pain and fear. She lashes out releasing a wave of TK/telepathic energy that crumples cars and uproots trees. The bystanders clutch at their skulls as they are knocked out by the psionic blast. Jean is alone amongst the destruction in a pool of blood.
Following this Xavier (and possible Eric) come see Jean. She's alone in her room, she lies on a floating bed and everything else in the room revolves around her at varying speeds. She shows no strain whatsoever using her powers.
We recall the death of Jean Grey as she began to realise that potential, through the eyes of Scott, everything is red filtered. He sleeps on one side of the bed he once shared with her, the other side is pristine.
It is 4 Months after the tragedy at Alkali Lake and the Mutant Registration Act was passed with a slim majority. Scott is haunted by dreams of Jean, and decides he can no longer stay with the X-Men, he feels responsible for Jean’s death and everything around the mansion reminds him of her. Professor Xavier tells him of a strange power surge felt in the Alkali Lake region and manages to convince him to stay to investigate it. He and Logan leave for Alkali Lake. Tension between the two as they both love Jean.
Storm has been made de facto leader of the team, now comprised of Nightcrawler, Rogue, Iceman, Colossus and Shadowcat. She leads them in a Danger Room session. Iceman is attracted to Shadowcat, and the untouchable Rogue can see this.
Xavier supervises this training session from the control room. We next see the Danger Room not full of X-Men, just a young Jean Grey. She’s performing a simple task with her telekinesis. But she becomes frustrated, and lashes out with a wave of TK that bends the walls of the Danger Room and rocks the control room.
Senator Kelly is invited by Valerie Cooper, Under-Secretary of Homeland Security in charge of Mutant Affairs, to a high level meeting to discuss the mutant threat. Dr. Bolivar Trask is also in attendance, his mutant detection hardware, designed and derived from the late Gen. Stryker’s files reacts to Kelly.
Trask arranges a meeting with Kelly. A prototype Sentinel attacks and subdues Mystique. Trask arrogantly tells her of the extent of the Stryker project as she attempts to evade the Sentinel. Every little detail of his schemes.
Thus Mystique discovers that the Stryker project was funded by Trask and went further than Alkali Lake and other parts of it have not been halted but instead expanded into a new Weapon X initiative, privately funded and now overseen by Dr Bolivar Trask, a colleague and friend of William Stryker with three branches: creation of mutant hunting sentient robots (Sentinel Project), genetic super-enhancement of ordinary humans (Human Juggernaut Project), and the exploitation of mutants for military means headed by a Dr Nathaniel Essex (Archangel, Psylocke transformations… X4 maybe).
She is taken to Alcatraz to be interrogated. She is held with the likes of Gambit, Avalanche and Juggernaut, whose kept under suspended animation. His trials have been halted due to the psychological instability of the subject, convicted murderer Cain Marko.
At Alkali Lake Logan and Scott see the devastation wrought by the surge of energy as the ground is scorched and the trees are dead. They soon find the cause, Jean, now dressed as she was when she supposedly died. She looks at them as if for the first time. Scott is speechless and overcome. Logan inspects her noting she looks like Jean and smells like Jean. He attempts to approach her. She flares up igniting a small radius and burning Logan’s front, before flying off. We see Logan heal. It’s very obvious she’s different. The pair realise they have to get back to tell Xavier immediately.
Mystique escapes from Alcatraz, using her cunning. She manages to get free of her cell but she knows she won’t be able to make it past all the guards alone. She let’s loose Avalanche and Gambit to blast their way out. She walks past the Juggernaut’s holding facility, she realises who it is and her nasty side can’t help but release him.
Magneto takes this as a cue to declare an all out war on humanity.
Magneto comes to Charles one last time to try and convince him that his way is right and to tell him that this time if he or his X-Men interfere then he will do what is necessary. He tells him of the new Weapon X initiative, over a game of chess of course. Charles is shocked but still rebuffs the idea of violent means. Magneto then tells him who exactly is the subject of the human enhancement experiments, Cain Marko, Charles’ abusive step-brother. Possible elaboration on why Cain hates Charles; Cain’s abusive father and his belief that Charles spied on his private pain.
They return to the mansion. Magneto tells Charles to tell them the truth about Jean, his first pupil. Again we are in Jean’s room as Charles tells them not so much of the power Jean possessed, but the power that possessed Jean. Xavier and Eric come see Jean. She's alone in her room, she lies on a floating bed and everything else in the room revolves around her at varying speeds. She shows no strain whatsoever using her powers.
An object flies at the pair, and Magneto deflects it (MAGNETO: You’re not the only one with gifts.) Then Magneto clasps at his throat as Jean chokes him with TK while simultaneously tearing memories from his mind, including those of the Holocaust. Charles tells her to stop, and when she doesn’t listen he makes her stop. The objects around the room fall to the ground, as does Magneto. Charles tells his X-Men he was forced to put psychic dampeners in Jean’s mind, Magneto muses that Liberty Island tore down those mental dampeners.
Juggernaut’s stasis has worn off, he breaks out of Alcatraz alone and he goes on a rampage through NYC heading towards Charles. Val Cooper orders the Master Mold of the Sentinel’s specifications changed to produce one that can detect and target Juggernaut. A Sentinel is launched with Juggernaut as the prime target. It is destroyed.
Magneto deems this is not his fight and states this is the result of humanity’s own stupidity before leaving. He returns to his lair. He is followed by Phoenix (who trailed Scott back to the mansion). She is confused and wants answers. Phoenix takes information from his mind by force, despite the helmet that is meant to block even Charles. Her telepathy is too strong. But this still leaves her with only patches of memory at best.
The X-Men are sent to stop Juggernaut, they attack to find that he is physically invulnerable. Rogue attempts to drain off his power and finds that it’s too much for her to handle. There’s nothing they can do to stop him. They do eventually get his helmet of and Xavier’s mind brings him down.