Madelyne always bore a striking resemblance to the (then) presumed deceased Jean Grey. Numerous individuals mistook her for Jean reborn. To make matters more suspicious, Madelyne's mind was closed to Professor X and she was the sole survivor of a mysterious plane crash, which occurred at the exact moment the Dark Phoenix committed suicide on the Moon, or so she thought.
In reality, she was a clone of Jean created by Mister Sinister. Mr. Sinister found that a union between the X-Men, Scott Summers (Cyclops) and Jean Grey (Marvel Girl), would produce a powerful mutant. Sinister hoped he could control such a mutant and use it to defeat Apocalypse.
At the time, Jean, actually the Phoenix, was acting reckless, so Sinister created a clone of her. Sinister's plot was to produce a child from the union of Madelyne and Scott, whom he believed would become a genetically superior mutant. To Sinister's disappointment, Madelyne had no life and did not develop any mutant abilities at puberty as he had hoped. Sinister left Madelyne in her incubation tube as a failed experiment.
It was at the moment of the Dark Phoenix's death that a spark of the Phoenix Force was accidentally bestowed on Madelyne's body and renewed Sinister's interest. After Dark Phoenix died on the moon, the Phoenix sought to return the "borrowed" portion of Jean's soul to her body which was in suspended animation. Jean instinctively rejected the Phoenix and it wandered the globe, lost. Eventually, it became attracted to Madelyne, since she was an exact genetic clone of Jean. The Phoenix Force searched for the next best thing, giving a spark of itself to Madelyne, granting her a life force and some of Jean's memories.
Madelyne met Scott in Alaska, while he was being introduced to his grandparents. From the moment of their first meeting, Scott was immediately attracted to Madelyne for her physical resemblance to Jean. Mister Sinister had also played a part as matchmaker, by giving Madelyne a personality he knew Scott would like and placing her where they were sure to meet, as a pilot for his grandparents. Sinister also gave Madelyne the name "Pryor" as a pun on her "prior existence" as a cell sample taken from Jean. Scott was amazed how much Madelyne was like Jean, even after being tricked for a short time, by Mastermind, into thinking she was Dark Phoenix.
After a whirlwind romance, Scott proposed to Madelyne on the deck of the Starjammer and Madelyne and Scott were married on the grounds of the X-Mansion. During their honeymoon in the Caribbean, Scott and Madelyne were attacked by a shark and a giant squid. This prompted Scott to choose retirement, realizing he would rather start a family than face a life of endless battles among the X-Men and the Starjammers.
Early in their marriage, Scott and Madelyne were flying a geological survey team across Alaska, when they ran into a mysterious storm that forced them to crash-land. Through Loki's Firefountain, all non super powered humans aboard the plane (including Madelyne) were endowed with mystical powers. As Anodyne, Madelyne could heal virtually any injury, illness, and physical-defect. Madelyne also used mystical healing powers to allow Cyclops to function without his protective lenses. When it was discovered that Loki's intentions were never altruistic and that his gift was badly flawed, as the cost of those powers was the loss of individual creativity and imagination, everyone went against him. His plans ended, Loki was ordered by Those Who Sit Above in Shadow to restore everyone to their original state. Loki spitefully removed all the powers he had granted and everyone who Anodyne had cured were also regressed back. During the incident, Madelyne revealed she was pregnant.
Scott returned to the X-Men after learning that Magneto joined. While he went on missions, Madelyne was left at the mansion. Madelyne felt that she and Scott were drifting apart after getting calls from other X-Men about her well-being but not her husband. While Scott was battling Fenris at the trial of Magneto, Madelyne gave birth to her son in the kitchen of the mansion, who she named Nathan Christopher Charles Summers - Nathan from an implanted suggestion by Mister Sinister in Madelyne, Christopher from Scott's father, and Charles from his father-figure.
Scott battled Storm for undisputed leadership of the X-Men. Maddie inadvertently used her mutant powers for the first time to influence the outcome of the battle, and after he lost, Madelyne convinced Scott to move with her back to a cabin in Alaska and live out their lives there, a subconscious suggestion implanted by Sinister — the remote location made it easier for him to study and if need be abduct the child.
During their time away, their marriage became strained and Madelyne resented the fact that Scott was rarely home and that he continued to miss Jean. Madelyne was also upset at the fact that Scott only married her because of her resemblance to Jean and that he only left to be with her and the baby because he lost in his bid to run the X-Men. Scott became very distant, even leaving Madelyne in the middle of the night. When the real Jean Grey was revealed alive, Scott abandoned Madelyne and baby Christopher to be with Jean and help found X-Factor in New York, despite her threats of him not being welcome back. Madelyne was heart-broken that Scott had left their family.
Maddie was hired to fly a cargo to San Francisco for a large sum of money and, at the last minute, decided to take Christopher with her. Mister Sinister, reacting quickly to Jean's return, aimed to eliminate Madelyne before the truth of her creation was revealed, and sent his Marauders to kill her and kidnap her son. Maddie used her latent psychic powers to defend herself, but lost baby Christopher to her enemies. Maddie was shot multiple times and left for dead, then taken to a hospital in San Francisco, as a “Jane Doe“. Though the doctors thought she was a hopeless case, Madelyne pulled through and awoke months later from a coma after having dreams of surviving a plane crash and the flamebird of the Phoenix. There was no record of Maddie or the baby left in existence, as Sinister had erased them all.
Death of the X-Men
Upon waking, Maddie called the X-Men and was confused why Scott left her and took the baby. When the Marauders returned to finish the job, the X-Men were present and protected her. As Madelyne felt abandoned, by Scott, Alex Summers, Scott's brother, was alone too, due to the fact that his lover, Polaris, was being controlled by the Marauder, Malice, and the two comforted each other.
In Dallas, Texas the X-Men battled the Adversary and gave their life to imprison the Adversary. Forge required the essences of nine souls to seal the portal and, with only eight X-Men present at the time, Madelyne agreed to be the missing piece and the group was transformed into pure energy. The entire incident was recorded by a news crew providing Madelyne with the chance to tell Scott she loved him and to find their missing son. However, the Omniversal Guardian, named Roma, restored the X-Men to life. After being resurrected, the X-Men decided to use the opportunity to go underground and keep their rebirth secret.
The X-Men resurfaced in Australia, where they defeated the Reavers and claimed their base and teleporter, Gateway, a mute, mutant aborigine with the ability to create gates with his bull roarer. Roma appeared and presented them with the Siege Perilous, a gem that created a portal which granted any person who walked through it judgment and a new chance at life, with a new career, home, and so forth and had magically made them invisible to any sort of mechanical perception. While the X-Men would go on missions, Maddie would stay at the base and familiarize herself with the computer systems and, while watching the news, Madelyne saw Scott with Jean. Finally, Maddie learned the reason why Scott had abandoned her and she fell unconscious. In her dreams, Maddie was approached by the demon, S'ym, who toyed with her self doubt and tempted her with great power. Madelyne slowly lost herself to the dark side of her personality and manifested a black tattered uniform.
After Storm abruptly left in the middle of the night, Maddie tracked her to the Savage Land and the X-Men departed. After responding to a fake emergency call from the Press Gang, Maddie flew a plane for the Australian Flying Doctors and was ambushed and taken to Genosha, with Jennifer Ransome and an infant. While in captivity, the demon, N'Astirh, attempted to contact Maddie, but she told him to try later. The scientists of Genosha could not decide if Maddie was a mutant or human and, when the Genegineer came to check on her, Madelyne's latent powers had killed all the Magistrates investigating her and destroyed her observation lab; they also mentally attacked a representation of Dr. David Moreau himself, but, when asked what happened, Maddie had no memory. Madelyne had broke herself out of her cell and was cradling the captured infant, when the X-Men arrived to rescue her. Lonely and angry, Madelyne instigated an affair with her brother-in-law, Alex.
After sleeping with Alex, Maddie agreed to help the demons S'ym and N'Astirh create a link between Earth and the extra-dimensional Otherplace, in exchange for locating the Marauders, to have the X-Men make them pay,and baby Christopher. Later, Madelyne and Alex had Gateway teleport them to New York’s Rainbow Room, where they shared a romantic evening. After returning home, Madelyne had Gateway teleport her to the grave-site of Jean, where she cursed Jean for her troubles and Scott for lying to her. While at the grave-site, Jean's parent showed, to show their respects, and Maddie turned them to demons. N'Astirh appeared and took Madelyne to the State Home for Foundlings in Nebraska, Scott and Alex's childhood orphanage, and, in the basement, revealed a laboratory and an incubation tube with her name on it. In the lab, Mr. Sinister revealed himself and bound Madelyne, explaining her existence as Jean's clone to her. After being told that he would experiment on her, Madelyne used her considerable power to break free of Mr. Sinister's bonds and N'Astirh presented her with her son, whom she began calling Nathan. As the Goblin Queen, Madelyne descended into madness after Sinister revealed she was only a tool modeled after Grey and returned to New York, where she battled X-Factor, blaming Jean and Scott for the misery in her life, and instigated a battle between the X-Men and X-Factor, having the X-Men under her demonic influence and believing that X-Factor was attempting to kidnap Nathan. When Scott attempted to assist Madelyne, Alex interjected, stating that Scott forfeited every right to Madelyne when he walked-out on her. When N'Astirh appeared and attempted to take Madelyne, Scott saved Jean and Alex rode-off to rescue Madelyne and the baby. After arriving at the Empire State Building, Maddie revealed herself as the Goblin Queen and asked if Alex would join her. Alex agreed to become her Goblin Prince. The Goblin Queen, briefly attacked Phoenix, an alternate reality daughter of Scott and Phoenix, who believed the Goblin Queen to be Jean.
After the defeat of N'Astirh, the Goblin Queen captured Jean and another battle was instigated between the X-Men and X-Factor. Dazzler and Longshot were influenced the most, being told that they were stars in the center stage and ordered to attack Death. Death was delivered to the Goblin Queen, where she began to corrupt him as well kissing him and connecting their pasts of being used by Apocalypse and Mr. Sinister. The Goblin Queen attempted to sacrifice baby Nathan and the other nine mutant babies atop the Empire State Building to finish N'Astirh's work and permanently open a gateway between Earth and Limbo, to spite Scott. The Goblin Queen locked herself, Nathan, and Jean inside a psionic barrier, where she explained her origins as Jean's clone. Both X-Factor and the X-Men's combined efforts seemed to be futile in an effort to break through the telekinetic bubble. Pryor-Summers and Grey fought one-on-one, with Madelyne unleashing a psionic force, intending to destroy both herself and her opponents. X-Factor and the X-Men protected each other and Madelyne was the only one affected, but, as she lay dying, she pulled Jean into her mind to die with her. Jean would have succumbed, were it not for the Phoenix leaving Madelyne at that time and returning to Jean. Jean was able to resist and, as Madelyne died, Jean recovered the part of her soul the Phoenix Force had mistakenly given to Madelyne.
Years past, in which Scott and Jean married and her son Nathan traveled to and from the future and became the man called Cable.
Resurrected and Impersonated
Later the powerful Nate Grey traveled to this world from Earth-295. His mind looked for a companion, and discovered the spirit of Madelyne Pryor on the astral plane. X-Man subconsciously gave the echo of Madelyne's psyche a new form. Madelyne remembered very little of her past. In Paris, she was lured away from Nate by Selene, who slowly took her to New York and met with Sebastian Shaw, suggesting a revival of the Inner Circle of the Hellfire Club. Selene presented Madelyne as Black Rook. She proved her value by winning a battle against the London Club's Red Rook Scribe, pulling the parasitic mutant Mountjoy out of the woman‘s body.
One night, Tessa attempted to probe Madelyne's mind, but was discovered. Madelyne angrily defeated Tessa and proved to be telepathic too, making Tessa forget the incident. Madelyne's memory was fully restored at last. She searched for Nate Grey but met Threnody instead, who revealed to her that even though she was walking around and breathing, she was actually still dead. Angered, she murdered Threnody.
She then found Nate with Jean Grey. In a battle, Nate chose to side with Jean over her. Nate and Jean discovered that Madelyne was a psionic ghost, subconsciously given form by Nate. Nate tried to re-absorb her, only to find that he couldn’t, as she had become independent.
Madelyne returned to Sebastian Shaw, with whom she began a physical relationship with. This was of great concern to Selene and Tessa.
While Cable was in the middle of his Askani meditation, his mother appeared to him on the Astral Plane. She explained her life story to him and proposed they join forces to destroy all mutants and rule the world together. After a heated discussion, in which Cable refused to side with her, they decided to meet at a neutral contact point in Alaska. Cable emerged from his meditation and formed an uneasy truce with his mother.
Madelyne later returned to Nate Grey's side, now with the ability to teleport. Nate didn't want her around at first, but he eventually started to come around to her. When Nate was attacked by Strikesquad: Gauntlet, a group of operatives wearing psi-shielded armor, Madelyne was buried alive by one of them. She managed to escape by teleporting, yet, as the battle had taken a lot out of Nate, her body rapidly became drained and withered. In no shape to carry out her plans, she departed Nate's side.
Later, a Jean Grey from an alternate universe posed as Madelyne to Nate for a short time, but the impostor eventually revealed herself. Nate Grey finally discorporated while fighting a being called the Harvester and was never seen again.
Sisterhood of Mutants
Madelyne seemingly returned again, identified by Scott at a Dazzler concert. Recently she formed a female version of The Brotherhood known as the Sisterhood of Mutants. She had recruited Martinique Wyngarde, her half-sister Regan, Chimera, Spiral and Lady Deathstrike, promising to resurrect a person of their choosing. But first they needed a test, so she had them steal a coffin in Tokyo, containing Psylocke's old body in which Kwannon died in and the real Psylocke. Using a magical ritual, they resurrected her old body and placed her mind in it. Explaining the procedure's real purpose afterward, the Red Queen reveals her promised resurrections to be untried and uncertain; this causes some of her members to react violently against her, but she convinces them to continue following her. The Sisterhood then commences a surprise raid on the X-Men's base, quickly neutralizing several of the main X-members. Recovering from the initial attacks, the X-Men force the Sisterhood (now including a brainwashed Psylocke) to retreat; but the entire battle is only a distraction that has enabled the Red Queen to steal something kept by Wolverine: a lock of hair from Jean.
While Mastermind and Lady Mastermind confronted Emma, Storm, Dazzler and Karma, Madelyne and the rest of the Sisterhood raced to the grounds of the Xavier Institute where Jean was buried. Domino was already there and held the Sisterhood off until the other X-Men arrived. During the battle, Madelyne unearthed Jean's coffin. Cyclops warned her not to take possession of the body inside, but she did so regardless. Madelyne then collapsed in agony. Cyclops revealed that he knew Madelyne would come to Jean's gravesite and had Domino remove her coffin and replace it with someone else's, knowing nothing less than Jean's body could contain her. Madelyne discorporated into nothingness.
Avengers vs. X-Men
Mister Sinister created a group of Madelyne Pryor clones in order to take away the Phoenix Force energies from the Phoenix Five (consisting of the Phoenix Force-empowered Cyclops, Colossus, Emma Frost, Magik, and Namor).Unlike the original Madelyne, none of the six appears to had the chance to show indications of individual personalities or free will, but instead appeared to follow Sinister completely. The Madelyne Pryor clones joined Mister Sinister's other clone creations in fighting the Phoenix Five and managed to defeat each one, one by one. They also were able to siphon some of the energy from the Phoenix Force, but they all were immediately killed by the entity itself.