Jean Grey begins to develop incredible powers that corrupt and turn her into a Dark Phoenix. Now the X-Men will have to decide if the life of a team member is worth more than all the people living in the world.
The X-Men are now seen as nationwide heroes after defeating Apocalypse, but a new problem arises when they head into space to rescue stranded astronauts, and Jean Grey is exposed to a powerful energy force that gives her the powers of the Phoenix. Although she is impressed by her new powers, she realizes she can barely control it.
After Jean learns her father is alive (after supposedly dying in a car accident with her mother), she learns that he willingly gave her up to Charles Xavier since he blamed her for the accident, as it was her powers that caused it. When the other X-Men arrive to get her back, Jean ends up hurting Quicksilver and killing Mystique before fleeing to the island of Genosha. She asks for Magneto’s help, but he turns her away after seeing her attack a team of soldiers. He is convinced to go kill her after Beast shows up to tell him that she killed Mystique.
Jean is found by Vuk, leader of the D’Bari alien race that was tracking the energy force that destroyed their home planet and later entered Jean’s body. Magneto and Beast head to NYC to kill Jean, but Charles goes with Storm, Cyclops, and Nightcrawler to stop her. After a fierce battle, Jean appears to forgive Charles for suppressing her childhood memories (which led to her turn to darkness), but they are captured by a government mutant containment group. The D’Bari attack the train with the mutants and kill the soldiers before the X-Men are freed and fight back. Vuk, who had absorbed some of Jean’s powers, comes to finish the job, but Jean fights back and destroys Vuk in outer space before seemingly being killed by the powerful blast.
The mutant academy is renamed in Jean’s memory, while Charles retires. He remains close friends with Magneto, while a shot of a flaming phoenix in the sky implies Jean is alive.
In 1975, eight-year-old Jean Grey inadvertently uses her telekinesis to cause a car accident that kills her parents. Shortly afterwards, Professor Charles Xavier takes her to Xavier’s School for Gifted Youngsters, where he mentally blocks the accident from her memories and helps her hone her psychic abilities.
In 1992, nine years after the worldwide devastation caused by En Sabah Nur, the X-Men respond to a distress signal from the space shuttle Endeavour, which is critically damaged by a solar flare-like energy. While the X-Men save all of the astronauts, Jean is stranded and ends up absorbing all of the energy into her body. Jean survives the event, and her psychic powers are greatly amplified as a result. At the same time, the mental block placed by Xavier is destroyed, and she accidentally attacks the mutants celebrating at Xavier’s school after a mental breakdown, passing out afterward. She later travels to her childhood hometown of Red Hook, New York, after discovering that her father is still alive. The X-Men attempt to take Jean home, but she injures Peter Maximoff and accidentally kills Raven Darkhölme and several local police officers before flying away.
Jean travels to the mutant refugee island of Genosha to seek assistance from Erik Lehnsherr in controlling her powers, but is turned away by Erik after she engages in combat with U.S. military forces tasked with her arrest. Jean meets Vuk, the leader of a shape-shifting alien race known as the D’Bari, who explains to her that she has been possessed by a force of cosmic power which wiped out the D’Baris’ home planet years ago. The power had consumed all those it came across, until it encountered Jean. Meanwhile, Hank McCoy, who feels betrayed by Xavier’s manipulation of Jean’s memories, allies with Erik and the mutant refugees to bring down Jean in New York City.
Upon learning of Erik’s plan to kill Jean, the X-Men confront him and his faction in New York. As they battle, Erik manages to infiltrate the building and confront Jean but is overpowered by her new abilities. Xavier then enters the building with Scott Summers. Jean attacks them until Xavier convinces her to read his memories – allowing her personality to resurface. Feeling remorseful, Jean asks Vuk to take the force from her; however, it quickly turns out that doing so would kill her. Xavier and Scott are able to prevent Vuk from fully absorbing the force from Jean, before both mutant factions, including Jean, are captured by the U.S. government and placed on a train headed towards a secret containment facility. The train is attacked by Vuk and her D’Bari forces. When the soldiers are overpowered by the shape-shifters, the mutants are freed from their restraints to combat the threat. Xavier confers with Jean within his mind, allowing Jean’s personality to gain control of the force within her. Vuk once again attempts to drain Jean of the force, but Jean unleashes her full potential and kills Vuk before disappearing into outer space.
In the aftermath of the incident, the school is renamed the Jean Grey School for Gifted Youngsters and Hank becomes their new dean; with Xavier having retired after decades of fighting for mutant rights. While settling himself in Paris, Xavier is reunited with Erik and reluctantly agrees to play a game of chess with him. As they start playing, a flaming phoenix appears in the sky.
1975 – Young Jean Grey (Summer Fontana) is riding in a car with her parents John (Scott Shepherd) and Elaine (Hannah Anderson). Jean uses her powers to change the song on the radio, but soon becomes overwhelmed with voices in her head and yells out for them to be quiet. This causes Elaine, who is driving, to lose consciousness and drive into the path of a truck, causing a major accident that kills Jean’s parents, but she is recovered from the wreck without any injuries.
At the hospital, Jean is met by Charles Xavier (James McAvoy), who tries to comfort her. He tells her that she has a gift, and what she chooses to do with it is entirely up to her. He brings her to his School For Gifted Youngsters where he hopes to shelter her and allow her to use her powers for good.
1992 – The space shuttle Endeavour launches but is soon caught in the path of what seems to be a solar flare. The President calls Charles to fly out there and recover the stranded astronauts. Raven/Mystique (Jennifer Lawrence) leads the X-Men – Jean (now played by Sophie Turner), Scott/Cyclops (Tye Sheridan), Hank/Beast (Nicholas Hoult), Ororo/Storm (Alexandra Shipp), Kurt/Nightcrawler (Kodi Smit-McPhee), and Peter/Quicksilver (Evan Peters) – into space for the mission. They encounter the shuttle and have Kurt and Peter teleport there and use Peter’s speed to get everyone together and back to the X-Wing. However, one astronaut notes that their commander is still stuck on the shuttle. Kurt teleports with Jean to get him out. She tries to use her powers to hold off the incoming flare while Kurt gets the commander back, but the flare consumes the shuttle with Jean still inside. She absorbs the energy from the flare, but she survives. Kurt returns to bring her back inside, and the X-Men return home to be hailed as heroes.
Upon returning to the academy, Charles dismisses the other students from classes. However, Raven talks to Charles about how he seems to not care about how his students are being put at great risk with these missions, and that he may be more concerned with the newfound adulation that the X-Men have gotten ever since they defeated Apocalypse.
Elsewhere, a trio of ships descend near a lake house where a dinner party is taking place. A woman, Margaret (Jessica Chastain), goes outside to investigate when her dog starts barking. She finds three aliens from the D’Bari race approaching her and then killing her and her dog before their leader, Vuk, takes Margaret’s form. She returns to the dinner party and kills everyone there. Later, Vuk meets with other D’Bari disguised as humans. They have been following the path of the solar flare and they know Jean is carrying its energy.
Hank does a reading on Jean’s energy levels, which happen to be off the charts. She seems to feel stronger, and the other students think she is so cool, that they have started calling her “Phoenix.” As she joins Scott outside to party with the students, Raven talks to Hank about potentially leaving the academy and living their own lives together, but Hank thinks they should stay there. Jean then starts to feel triggered by the campfire that the students set up, and it causes her to lose control of her powers, sending a wave that knocks everyone back.
Charles goes with Hank and Raven into Cerebro to look inside Jean’s mind. There, Hank and Raven learn that Charles suppressed Jean’s memory of the car accident in an attempt to protect her from the pain and any guilt she may have felt. An unfamiliar voice is heard, and it causes Jean to wake up and pull Charles out of her head. Scott goes by her room to check on her, and she says that she knows her father is alive.
Jean goes to her old neighborhood and finds John is indeed alive and living alone in their old home. He invites her inside, but she sees that he only has pictures of himself and Elaine, and none of Jean. She looks inside John’s mind to find a memory where John willingly gave Jean up to Charles, as he blamed her for Elaine’s death and says that Jean and his whole world died that day. Jean becomes enraged, but the X-Men arrive to get her back and help her. She goes outside to confront them, with Hank trying to shoot Jean with something that will knock her out. Police arrive on the scene, and Jean wrecks them with her powers. She is too fast even for Kurt or Peter to catch her, and she ends up severely hurting Peter. Raven attempts to approach Jean to calm her down, but the moment Raven touches her, Jean releases a blast that sends Raven back and impales her on broken wood. Jean retreats while Hank attempts to help Raven, but it is too late.
The X-Men bury Raven and mourn her. Hank calls Charles out for what he did to Jean, claiming it’s his fault she became what she is, as well as for what happened to Raven. Later, Charles is even turned away by the President’s staff when he tries to ask for help.
Vuk and her associate, Jones (Ato Essandoh), arrive at the ruins of the neighborhood. Vuk enters John’s home, and after a few words, she kills him by tightening his chest.
Jean travels to the island of Genosha where she finds a mutant sanctuary led by Erik/Magneto (Michael Fassbender). She wants protection, but Erik is suspicious as he spots Raven’s blood on Jean’s shirt, and she won’t say whose it is. Moments later, a military team descends upon the island, and the captain talks to Erik about giving Jean up. She emerges and tries to kill the soldiers by pulling their chopper blades toward them, but Erik holds it off long enough for the soldiers to get away unharmed. Erik orders Jean to get out.
Vuk walks into a bar and finds Jean disguised as a projection of an old man. She convinces Jean to join her, and Vuk takes her to her hideout with the other D’Bari. Vuk shows Jean a projection of the events that gave her her powers. The D’Bari were tracking the power source that destroyed their home planet, and they witnessed Jean absorbing it. Vuk convinces Jean that the other X-Men will try to destroy her since they cannot control her.
Hank flies to Genosha to ask for Erik’s help. He tells him that Jean killed Raven, which is enough to convince Erik to hunt Jean down and kill her. Erik is helped by another telepathic mutant, Selene (Kota Eberhardt), who tracks Jean’s location to New York City.
Scott, Storm, and Kurt approach Charles after learning that Erik and Hank are going after Jean. Although he doesn’t want them going after her, they go against his orders, and he has no choice but to join them. They head to NYC where Erik, Hank, Selene, and another mutant, Ariki (Andrew Stehlin), arrive to kill Jean. Both mutant groups fight each other in the streets amidst frightened civilians. Selene pulls Kurt away as he tries to teleport into the building where Jean is. Erik makes his way into the building, but his attempt to kill Jean fails, and she nearly kills him by tightening his helmet and then breaking it into sharp pieces that pierce him and knock him out. With Storm’s help, Charles is able to fight off Selene and Ariki to get into the building. Jean manipulates Charles’s body to walk upstairs to confront her, but he apologizes for tampering with her mind, and he lets her look into his mind to show the memory of when John gave her up to Charles. He never gave up hope on Jean, and it is this that lets her good side return. She starts to relinquish her powers to Vuk, who then announces her intention to destroy humanity and take over their planet, but they are interrupted when the Mutant Control Unit arrives to tranquilize all the mutants and capture them (yes, the MCU is taking the X-Men away).
The mutants are put on a train to a facility for containment. The D’Bari then attack the train as they try to get Jean back. The mutants are freed but the soldiers start to get killed by the D’Bari. They fight off the aliens one by one, with Selene and Ariki getting killed in the process, but Kurt, Erik, Storm, and Hank make good uses of their powers to destroy most of them. Vuk, now more powerful, comes to get Jean, and none of the other mutants can hold her back. Charles goes to Jean and gets her to wake up. She protects the mutants as she destroys the train. Vuk attempts to take the rest of Jean’s powers, but Jean starts to willingly do so as she can see it is overwhelming Vuk. The energy from this starts to cause Scott to disintegrate, and Vuk reminds Jean that she can’t kill her without harming the others. Jean then pulls Vuk above Earth and obliterates her there, leading to a blast that causes Jean to vanish while leaving a flaming phoenix in the sky.
Later, the academy is renamed Jean Grey’s School For Gifted Youngsters. Hank becomes the new dean while Storm becomes a teacher, and Peter has recovered from his injuries. Charles retires and goes to Paris, where he is found by Erik. He offers to play a game of Chess with Charles, who at first declines, but then comes around after Erik says he wants to do what Charles did for him many years ago, which is saving his life and giving him a home. They start playing, and the last we see is a flaming phoenix soaring through the sky.