JEAN GREY's arc ESSAY Part I.Firstly, the movie
Jean Grey/Phoenix exists in a different continuity to the comic's, as do all the characters who appear in the movies, so there are several creative differences between them (eg - Havok being the older brother of Cyclops, when its vice-versa in the comics, Mystique growing up with Charles etc).
While the comic Phoenix is a separate entity to Jean Grey, The movie Phoenix is Jean's full potential, and Xavier's inadvertently created The Phoenix persona as a separate personality because of his mental blocks, at least that was true in the original timeline...
So here's the movie explanation of Jean Grey/Phoenix.
As seen in a flashback in
"Last Stand" shows Jean as a young girl, using her vast powers of telekinesis to lift multiple cars in the neighborhood, and even to cause water to flow upwards instead of downwards, displaying how incredibly powerful she is at a pre-teen age.
Sometime before the events of the first film, Charles decides to erect mental blocks in Jean's mind, to siphon away the majority of her powers (we do not know the exact event that lead to him choosing this option, but expresses to Wolverine in
"The Last Stand" that he had a terrible choice and made the lesser of two evils).
As seen in
"X-Men" Jean is a low powered mutant with dual abilities of telekinesis and telepathy. She is notably the weakest member of the X-Men, barely able to levitate a chair or book across the room, with her greatest feat in the movie - stopping Toad midair. After her ill advised use of Cerebro or her exposure to Magneto's mutation machine, Jean appears to be visibly shaken and it is thought that her powers have increased.
During
"X2" Jean has grown considerably in power, her own powers are now becoming so powerful, Xavier's control is starting to weaken. Jeans powers cause her to hear the thoughts of hundreds of people, causing several minutes of electric failure and mayhem in the localized area, as well as psychic precognition, and later the ability to stop mutants like Nightcrawler using his powers. When the X-jet is attacked by the government, Jean attempts to destroy the two missiles on route to destroy the ship, as Jean struggles to concentrate on her target, her eyes are engulfed in flames and one is destroyed, as she frantically tries to destroy the second, her powers fail and the Jet is hit, sending the team plummeting towards to ground...
As the film continues, Jean displays a greater use of her telepathy, allowing her to find out were Stryker's base is from Nightlcrawler and to anticipate and attack from a mid controlled Cyclops, thereby saving Magneto and Mystique. Jean and Cyclops do battle, with the latter blasting Jean with full power - Jean is able to project a telekinetic shield that protects her from the blast but pushes her further and further back, as she begs Scott not to do this, the Phoenix persona overtakes Jean and absorbs the full power of Scott's optic blasts and scatters the beam, causing massive damage in the surrounding area, releasing Scott from the mid control and having the unwanted effect of causing the damn to rupture. After the team escapes the damn, and eventually gets back on board the Jet, Jean has a premonition about what is about to happen, realizing that they will all die, Jean makes the heartbreaking choice to sacrifice herself to save the team, she exits the Jet, and uses her powers to seal the Jet from the outside, blocks the mutants from using their powers to rescue her, takes control of the jet, both electrically and physically, uses her TK to stop the torrent of water from the recently erupted damn, that thretens to drown them all, and lift the team to safety, becoming engulfed in a fiery aura - The Phoenix. As the team realize what has happened, Jean allows herself to be killed by the water, and they escape to safety. Jean is later seen as a fiery bird under the water of the lake that the destruction of the damn created.
After the events of X2, the X-Men, and in particular Scott, are struggling to come to terms with Jean's death. Made harder by the fact that Jean appear's to be tormenting Scott, as he sees visions of her when he is asleep. Deciding he wants closure, Scott travels to the lake where Jean died, angry at the world, he angrily unleashes his optic blasts, he watches confused as the water swirls around, in what appears to be a whirlpool, a blinding light causes him to be knocked backwards, as he arises, he struggles to see a figure emerging from the light... Jean Grey.
The couple embrace, both appear to be confused as to how this is happening, Jean removes Scott's optic visor, and proclaims that she can control his power, apprehensive Scott reluctantly opens is eyes, and is shocked that Jean was right, as the couple embrace for a kiss, Jean's eyes become black and her skin produces black-green veins, and she kills and destroy's Scott in cold blood.
This display of power alerts Xavier to Jean's presence. So sends Storm and Wolverine to investigate, who find an unconscious Jean, as well as Scott's visor, but no sign of Scott.
Xavier uses his powers to keep Jean subdued, noting that her own powers are fighting to regain control, here he explains that Jean is a class 5 mutant, immensely powerful, and that he erected mental blocks at an earlier point in time to "cage the beast" - an incredibly powerful entity was created because of this - that became known as the Phoenix - its sole purpose was fueled by rage. Due to Xavier, the Phoenix and Jean were two separate personality's. Wolverine, horrified that Xavier is the cause of Jean's instability, proclaims that "when you cage the beast, the beast gets angry" Xavier defends himself saying that he had a terrible choice and that he made the lesser of two evil's, and continues to try and subdue the Phoenix from emerging again.
Later, Wolverine is alone with Jean, who wakes and converses with him, she begins to seduce wolverine, using her TK to remove items of his clothing, as the two embrace, The Phoenix takes control and once again her eyes turn black and veins appear on her face, using her power to cause rips in Wolverine's flesh, he shows her Scott's visor, causing Jean to retake control and realize that she killed Scott, her powers become unstable and causes the room to shake and medical instruments to float in the air, as Jean sobs, Wolverine mentions the professor - this angers the Phoenix who declares that Xavier is in all their heads, and it retakes control of Jean, it then flings Wolverine against a wall and disintegrates the door to the medical lab, walking out and fleeing the school.
Xavier locates Jean at her childhood home, but Magneto was also alerted, by a mutant that can sense others powers, saying that this is like nothing she has felt before and that it is more powerful than even Magneto, knowing exactly who she is describing, Magneto asks "Where is she"?
Both men attempt to convince Jean to join them, both arguing that Charles treated her as a child, when in reality she is a "goddess", as Xavier attempts to use his powers to get through to Jean, this angers the Phoenix, who throws Magneto into the kitchen, and uses her TK to lift Xavier up and disintegrate him - literally tearing him apart on a molecular level, killing him. A confused Jean then leaves with Magneto.
Later, Magneto attempts to appeal to the Phoenix, to get her to join their fight against humans, showing Jean a gun, whose bullets will remove the powers of anyone it hits, The Phoenix taunts Magneto, breaking the gun apart and using TK to aim the bullets at Magneto, who is horrified and commands her to stop, The Phoenix eventually complies and states that Xavier and Magneto are exactly the same - they both want to control her.
At the films climax, the X-Men battle the Brotherhood, with Jean Grey stood watching and not participating, as the X-Men win, and use the bullets to depower Magneto, Wolverine appeals to Jean to re-join the X-Men, Jean is about to accept when the human army mistake her for a threat and open fire, firing hundreds of power blocking bullets at her, the Phoenix once again emerges, angry at everyone, The Phoenix uses TK to stop the bullets from getting near her and proceeds to disintegrate hundred of humans and mutants alike, with very few people escaping her powers, knowing that there is only one way to end this, Wolverine advances towards Jean, his own power of regeneration providing him limited protecting from The Phoenix's destructive powers, as he gets closer to her, The Phoenix states that "He (Wolverine) would die for them?" to which Wolverine responds "No... not for them" this declaration of love allows Jean to retake control, begging Wolverine to Kill her, he complies and all the destruction is stopped.
In
"X-Men: Days of Future past" Wolverine's trip to the past, altered the future, e told Charles to look out for Jean, and even showed him visions of what the original timeline was like, showing him what Jean will do with her powers, this likely caused Charles to alter his plans for Jean and allowed her to develop the Phoenix naturally, and in the altered future, Jean and Scott were alive. While it is noteworthy, that Jean had red hair in this future, when before she had access to the Phoenix powers, her hair was brown, so it can be assumed that while Jean does have access to the Phoenix powers, the events of the first three films have been significantly altered, so much that Jean and the Phoenix were one (the duel personality it what ultimately lead to Scott's and her own death).
The Jean Grey in
"X-Men: Apocalypse" has many of the powers associated with the Phoenix (fire, pre-cognition etc) as well as her well known powers of Telekinesis and telepathy. We learn that Jean is a somewhat confident young woman who is ostracized by her mutant classmates because of her vast powers, finding comfort with new student Cyclops (who is also feared for his powers) the two accept that they are feared because of their powers and aim to support each other. Jean continues to grow in confidence, becoming the de-facto leader when Mystique is subdued, she effectively commands the team to rescue Xavier and orders them to leave after they have him (knowing that Apocalypse is vastly to powerful to stop), their escape is short lived when Archangel and Psylocke attack the Jet, bringing the vehicle down and they are forced to hide in the ruins of Cairo, Jean and Nightcrawler protect Xavier's body while he telepathically fights Apocalypse, and Mystique, Quicksilver, Cyclops and Beast fight him physically as well as battling his Horsemen. With both groups barely causing any damage to the god like Apocalypse, who uses his exceptionally powerful shield to protect him from all the powers of the X-Men and even overpowers Xavier in their telepathic battle, seeing the destruction Apocalypse is creating, and spurred on by Xavier to unleash her powers (a marked change form the original timeline, Xavier wanted to contain the Phoenix, NOT unleash it) Jean unleashed her true potential and uses TK to levitate herself towards Apocalypse, using her vast powers Jean rips the armor from Apocalypse's body (bypassing his shield, that was impenetrable by lightning, optic blasts and tons of metal) and proceeds to disintegrate Apocalypse on a molecular level, while unleashing the fiery bird aura that the Phoenix is famous for, thereby destroying him. While no other mutant could cause any damage to Apocalypse, he protected himself from all their powers and was even able to adapt to Quicksilvers speed and stop him, Jean was the only one who could hurt him and definitely the only one who could kill him.
So in the original Timeline The Phoenix was a separate personality inadvertently created when Xavier erected mental blocks to control Jean's powers, this personality became vengeful and dark, and contained a large portion of Jean's powers, while they are separate, there are occasions when they united (plane attack, Cyclops attack etc) and Jean could use all of her incredible power, but this was only temporary, and once Jean became unstable, the Phoenix would assert control again.
However, because Xavier was warned by the future Wolverine about Jean, he made different choices, highlighted in "X-Men: Apocalypse" and as such, the Phoenix has been allowed to develop naturally inside Jean and there is no duel personality. Meaning Jean has access to the vast array of powers her future self would have had as the Phoenix, but without loosing control, and at a much early point in time, meaning Jean Grey/Phoenix is now one in the same and not two separate entities.