Magneto and Professor X arrive at the Greys' home, meeting a young Jean Grey. The powers of the little girl are beyond imagination, and, while Lensherr wants to use them, Xavier fears them and decides to create mental blocks to restrain them.
Jean Grey is one of Professor X's first students and one of the first X-Men. After years of school together, she begins a relation with her teammate Cyclops.
When Wolverine and Rogue are attacked by The Brotherhood of Evil Mutants and saved by Cyclops and Storm, Jean Grey is the one who cures them once in the X-Mansion. When Wolverine awakes, he's confused and feared and attacks Jean before fleeing. When Professor Xavier has explained to Wolverine the situation, he comes to Jean for making his excuses. The two have a talk, with Wolverine putting Jean's power to a test and teasing her, thus provoking Cyclops' jealousy.
When Xavier is made unconscious by Mystique's poison, Jean uses Cerebro to track down Rogue and Magneto, but her powers aren't powerful enough to use it and, even if she manages to locate them, the machine drains her out making her faint, and erasing the mental blocks Xavier built for restraining the Phoenix.
When the X-Men arrive on Liberty Island to fight the Brotherhood, Jean fights against Toad, yet Toad turned the tables on Jean spewing a thick phlegm-mucus-slime onto her face in which she struggles for oxygen and is found by Cyclops to much of his horror, he saves her by blasting the encrusted slime away. Once on the top of the Liberty Statue, Jean is captured by Magneto with the other X-Men, but manages to break free using her powers and Scott's. She then uses her telekinesis to send Wolverine to Magneto's machine, so freeing Rogue moments before Brotherhood's plan is accomplished. After the mission, she gives cure to Xavier, assisting him until he's healed from the poisoning. With Magneto captured and the Brotherhood disbanded, Jean can restart her usual life in the school as a teacher.
Jean Grey has restarted her life as it was prior to Magneto's treat, but something has changed: her powers has increased drastically since the day she used Cerebro, and Scott is starting to get worried about their extent: when Jean has some nightmares, infact, she's powerful enough to shake the entire room.
After Nightcrawler's attack to the President, Jean and Storm are sent to track the mutant and bring him to Professor X. Just for testing her new abilities, Jean drives the X-Jet with her powers, thus making Storm worried about her conditions. The two X-Girls find Nightcrawler in an abandoned church and learn from him that he was forced to attack the White House while under some kind of mind control. Nightcrawler joins the two, and they all together comes back home. On the way to the X-Mansion, Jean and Storm discover that the school has been attacked by William Stryker's men and that the students are prisoners of Weapon X. Intercepting a call from Wolverine, Jean and Storm picks up him and three students (Rogue, Iceman and Pyro) just before they cause too much damage to the Boston police. In flight, the X-Jet is attacked by two F-16s, and Jean uses her power to destroy the missiles they have launched, with her eyes starting to glow with a strange red light. One of the missiles manages to hit the jet, and the X-Men are saved by Magneto, who offers an alliance against Stryker. During a briefing, the former enemies share the respective informations about Stryker and his group, and decides for an attack to the Alkali Lake base.
In the base, Jean fights with a brainwashed Cyclops, and she manages to defeat him surpassing the limits of her powers, becoming surrounded by a red, fiery aura. After the battle, the X-Jet is damaged and can't leave the place before the dam bursts. Jean makes a decision, and leaves the jet: using her powers, she stops the flood and raises the jet on the water, then she activates the main engines and makes her teammates flee, just a moment before releasing the flood on herself. All her teammates believe Jean's dead, but, deep under the waters of Alkali Lake, a phoenix-shaped light begins to glow.
Depressed by Jean's death, Scott Summers goes to Alkali Lake to mourn his loss. Once here, he releases a powerful optical blast in the lake, and the ray breaks a telekinetical coccoon built from the Phoenix at the bottom of the lake. Jean Grey lives again, and reaches her beloved on the shore. She takes his glasses, managing to contorl Scott's power with hers, and the two share a kiss, looking one in each other's eyes for the first time. During the kiss, Jean abandons herself to instinct and accidentally kills Scott. Worried for Cyclops, the other X-Men arrive on the shore, finding Scott's glasses floating in the air with stones and logs. A little distant, they find Jean, fainted, and, surprised, they take her back to the X-Mansion. Once there, she tries to seduce Wolverine, but when he refuses her and tries to know about Scott, she expolodes: after attacking Logan, confused and angry, she escapes the Mansion and comes back to her childhood home. In here, she's reached by both the X-Men and The Brotherhood of Evil Mutants, who start a fight while Xavier and Magneto try to convince Jean to join their respective sides. When Xavier tries to block her powers again, the Phoenix gets enraged and unleashes all her might, making everyone fly away, destroying her home and killing Professor X. Confused and saddened by her mentor's death, Jean follows Magneto to his hideout. Wolverine follows them and tries to talk with Jean, but the Phoenix personality is storng and sends him flying in the woods.
Magneto believes he can use the Phoenix's powers for his aims, and brings her with him to Alcatraz Island to destroy Worthington's facility. During the battle that follows X-Men's arrival, Magneto tries to make the Phoenix join the battle, but she's not interested, not even when Magneto is depowered by the Cure. Wolverine almost manages to make Jean's personality resurface, but the human soldiers intesify the fire on all the mutants, Phoenix included, so unleashing her rage. The Phoenix starts a massive attack on everything and everyone, destroying Worthington's facility and killing human and mutants on her way. While everyone is forced to escape, only Wolverine manages to go near her, since his healing factor prevents her from pulverizing him. When the Phoenix angrily asks him: "Would you die for them?", Logan replies "Not for them. For you." In that very moment, Jean resurfaces for a moment and begs Wolverine to stop her. In tears, declaring his love to her, Wolverine stabs Jean Grey, killing the Phoenix and putting an end to the destruction. Jean's grave is put near Scott's and Xavier's, so reuniting them in some way.
Jean Grey is a powerful mutant, who posses vast, potentially limitless telepathic and telekinetic abilities. As the Phoenix, her telekinesis is powerful enough to move the single atoms, so giving her the possibility to literally disintegrate anything. Her telepathy is such that she has the ability to exceed even Charles Xavier in mental power.
She's a gentle and motherly woman, responsible and with some leader abilities. She's in love with Cyclops, but she doesn't dislike flirting with Wolverine, both of them representing two different aspects of her own personality, the loyal and noble one and the savage and animalistic one. As the Phoenix, her character changes completely, and she becomes a violent and confused person, always abandoning herself to emotions and instinct.