Charles Francis Xavier was the mutant son of wealthy nuclear researcher, Dr. Brian Xavier, and his wife, Sharon Xavier-Marko. While gestating in his mother's womb, Charles' twin was recognized by Charles as an evil presence and he preemptively tried to kill it with his nascent psychic abilities, causing the fetus' miscarriage. After Dr. Xavier's death in an accident, Sharon married his colleague Dr. Kurt Marko who brought his son by a previous marriage, Cain Marko to live in their ancestral mansion. Dr. Marko favored the gentle, smart Charles over his own son, which led to Cain bullying Charles and Dr. Marko secretly beating Cain. Sharon married Dr. Marko because she believed that it would be best for Charles.
Charles' telepathic powers began emerging when he was still a boy, around ten, and, as he grew older, he learned to control them. Due to the immense psychic energies emanating from Charles' head, he became bald at a young age. With his powers, Charles had discovered that Dr. Marko cared only about his mother's money, admitting that he was jealous of Dr. Xavier's wealth. Dr. Marko quickly grew neglectful of Sharon, driving her to alcoholism, and abused both Sharon and Cain. Charles linked his mind to his mother's, in a effort to share the abuse with her and alleviate it. Charles, on one occasion, found himself experiencing the anguished thoughts and emotions of Cain, after Cain had been beaten by his father, which only led to Cain becoming more aggressive toward him and Charles feeling Cain's pain firsthand, but the inexperienced young Charles could not control or end his contact with Cain's mind at this time. Sharon died shortly thereafter, of a broken heart, leaving Charles to live with his step-father and abusive step-brother.
Later, a fight erupted between Cain and Dr. Marko, that caused some of Dr. Marko's lab equipment to explode. Mortally wounded, Dr. Marko dragged the two children out before dying, begging forgiveness for not saving Dr. Xavier when he had the chance, and telling Charles to keep his powers secret from Cain. Cain was standing over them and heard of Charles' gift, which led him to believe that Charles had invaded his thoughts deliberately. From then on, Cain regarded Charles as his enemy.
A brilliant student intent on undertaking graduate studies, Charles entered England's Oxford University, where he met and fell in love with a young Scotswoman named Moira Kinross while Cain continued to live at the mansion. Cain grew increasingly resentful of his step-brother's scholastic and athletic achievements, as well as his telepathic powers and even pushed Charles too far one day and the two got into a fight, which Charles easily won. Moira and Xavier's passionate discussions on genetic mutation gave way to an equally passionate romance. It had also been hinted that Mister Sinister interfered with Moira and Xavier's relationship, as he was posing as a professor at Oxford at the time. Charles and Moira planned to be married, but after finishing his work at Oxford, Xavier was drafted and sent to Asia during the Korean War. There, Xavier and Cain served in the same unit. Attempting to bring back the deserting Cain, Xavier witnessed how Marko found the mystical ruby in the Temple of Cyttorak, that transformed him into the superhuman Juggernaut. Just then, enemy high explosive bombardment caused a cave-in and Marko was buried under several thousand tons of rock. Xavier survived and returned to his unit. Xavier also served alongside Kitty Pryde's father, Carmen Pryde, on search and rescue missions, where he earned the nickname, the Good Shepherd.
Deeply depressed when Moira broke off their engagement without explanation, after inheriting his family's considerable wealth, Xavier began traveling abroad. After leaving the army, Xavier later discovered that Moira married her old boyfriend, Joseph MacTaggert, who abused her. While in Cairo, Egypt, Xavier met the young pickpocket, Ororo Munroe, and, while making mental contact with her, battled Amahl Farouk, the Shadow King host, the first evil mutant he had ever met. This meeting led to the visionary Xavier's decision to devote his life to protecting humanity from evil mutants and safeguarding innocent mutants from human oppression, believing that both could peacefully coexist. Xavier, who acknowledged she was a mutant from her brainwaves, declined to contact Ororo at this point, not wanting to shock the young woman with the true nature of her powers.
Xavier next went to Haifa, Israel to meet with the head of a clinic for traumatized Holocaust victims, Daniel Shomron, where he fell in love with the catatonic Gabrielle Haller, whom he awoke using his telepathy, and became friends with a man calling himself Erik Magnus Lehnsherr, a volunteer. Magnus and Xavier held lengthy debates hypothesizing what would happen if humanity was faced with a new super-powered race of humans, unaware that Magnus himself was a mutant. While Xavier was optimistic, Magnus' experiences in the Holocaust led him to believe that humanity would ultimately oppress the new race of humans, as they had done with other minorities. The two friends revealed their powers to each other when they fought Nazi Baron von Strucker, and his Hydra agents, who kidnapped Gabrielle because she knew the location of their secret cache of gold. Magnus attempted to kill von Strucker, but Xavier stopped him. Realizing that his and Xavier's views on mutant-human relations were incompatible, Magnus left with the gold. Charles stayed in Israel for some time, but Xavier and Haller were unaware when he left that she was pregnant with his son, who would become the autistic mutant known as Legion, and they separated on good terms.
In a strange town near the Himalayas, Xavier encountered an alien calling himself Lucifer, the advance scout for an invasion by his race, and foiled his plans. In retaliation, Lucifer dropped a huge stone block on Xavier, crippling his legs. Xavier was freed by Sage who had heard his telepathic cries for help. Xavier went into a deep depression after losing the use of his legs and Amelia Voght, a young American nurse, made cheering him up her pet project. Amelia helped Xavier recover during his convalescence in Bombay, India, wherein the two fell in love. While living in an apartment together in Bombay, Amelia found Xavier's notes of a device, called "Cerebro", that could detect mutants. Amelia fought with Xavier, believing that he only wanted her as an experiment, until he used his power to speak in her mind that he loved her. Realizing that he, too, was a mutant, the couple grew very close and Xavier continued his dream with Amelia by his side.
Xavier worked with fellow mutation expert, Dr. Karl Lykos, as well as Dr. Moira MacTaggert, who built a Mutant Research Center on Muir Island, again. Apparently, Charles had gotten over Moira in his travels to the Greek island of Kirinos. Xavier renewed his friendship with Moira, who was now a renowned geneticist, and they began discussing the idea of founding a school for mutants. Xavier discussed his candidates for recruitment to his personal strike force, the X-Men, with Dr. MacTaggert, including those he passed over, which were Kurt Wagner, Piotr Rasputin, Pietro and Wanda Maximoff, and Ororo. Professor Xavier's first student was the 11-year-old Jean Grey, who had been traumatized when she telepathically experienced the emotions of a dying friend. Over the years, Charles made a name for himself as geneticist and psychologist, renowned enough that the Greys were referred to him when no other expert could help their catatonic daughter, Jean. Professor Xavier helped Jean recover and taught her to use her telekinetic powers. Professor Xavier also trained Tessa to spy on Sebastian Shaw and built a machine for Jamie Madrox to learn at home, instead of going to school.
Professor Xavier later met with Fred Duncan, an FBI agent investigating the growing number of mutants. Professor Xavier told Duncan of his plan to locate young mutants and enroll them in his "School for Gifted Youngsters", using his ancestral mansion home as a base to train them to use their powers, as well as provide them conventional educations, for humanity's benefit. The base included subterranean medical labs, a training facility called the "Danger Room", an aircraft hanger with a Stratojet, and Professor Xavier's mutant detection device, code named "Cerebro". Amelia stayed with Professor Xavier, partially because she loved him, but also to convince him to give up his nonsense idea. On the anniversary of his liberation from the Vernichtungslager Extermination Camp, Professor Xavier and Amelia met with Erik, now calling himself Magneto and in costume and helmet designed to shield from telepathy, in Auschwitz, Poland. Professor Xavier pleaded with Magneto that the actions he would set into motion were no different than what the Nazis did to him years earlier. After both men reminded each other that they had the power to destroy each other, Magneto left, with Professor Xavier hoping that he saw the error of his ways.
Amelia left Professor Xavier as Scott Summers moved into the mansion, believing the best solution to the "mutant problem" being for mutants to lay low. Professor Xavier tried to force her to stay with his mental powers, but immediately ashamed by this, let her go. Over the following months, Professor Xavier assembled his original team of X-Men: Scott, who took the name Cyclops, Iceman, Angel, Beast, and Jean, who took the name Marvel Girl. The first menace they would face was Xavier's old friend Magneto, now a mutant supremacist and his Brotherhood of Evil Mutants.
After training them for several years, Professor Xavier went underground from all of his original students, save Jean, to prepare for the invasion of the alien Z'Nox and had the reformed and dying villain, Changeling, posing as him after giving him a portion of his telepathic power. The X-Men disbanded after Changeling was killed by Grotesk and Professor Xavier left all of his belongings to Scott. Professor Xavier returned with Havok and Lorna Dane to stop the invasion of the Z'Nox, where Prof. Xavier probed every human mind on the planet and was left in a weakened state, and was revived using a device created by Bruce Banner.
Second and Third Team of X-Men
Years later, when most of his original students were captured by the mutant island Krakoa, Professor Xavier sent another team comprised of Dr. MacTaggert's students, Kid Vulcan (who was Cyclops' unknown brother), Petra, Darwin, and Sway, all of whom he gave quick, mental combat experience, to rescue them. Professor Xavier also approached Emma, to be the team's telepath, but she refused and the Professor erased the event from her memory. After the team freed Cyclops and Kid Vulcan revealed their connection, the entire team was seemingly killed. Cyclops escaped, but, when he made it back to Professor Xavier, the Professor wiped the traumatizing knowledge that his new-found brother had died saving him from Cyclops' memories. Professor Xavier assembled another team of X-Men, including Banshee (former Factor Three operative), Colossus, Nightcrawler, Storm, Sunfire, Thunderbird, and Wolverine to rescue the others on Krakoa, never revealing anything about Dr. MacTaggert's students. The mission was successful and the team stayed together, save Sunfire.
Their next mission was to stop Count Nefaria and his Ani-Men, during which Thunderbird was killed attempting to stop Count Nefaria's escape. The team went on to battle Kierrok and Professor Xavier was captured by Steven Lang's Sentinels and taken to his space station, until his X-Men rescued him. After, Professor Xavier stayed with a weak Jean in the hospital, after she had piloted the shuttle back to Earth and declared herself the Phoenix. At this time, Professor X had somehow also gained access of a RS-150 Blackbird from S.H.I.E.L.D., as the X-Men's new transportation. Lilandra Neramani, princess of the alien Shi'ar race and the woman he shared an intense psychic bond with across the vast distance that separated their two planets, came to Earth to implore Prof. Xavier for his help against her mad, tyrannical brother, D'Ken Neramani, and he, instantly, aided her by deploying his X-Men. They, then, journeyed to the M'Kraan Crystal's homeworld to battle the Shi’ar Imperial Guard.
After briefly battling Weapon Alpha, and, later, Warhawk, Phoenix returned from the Savage Land to tell Professor X that all the X-Men were dead. Prof. Xavier shut down the school and traveled with Lilandra to her kingdom, where she was crowned Empress. Prof. Xavier dreamed of her and Lilandra knew they were soul mates. They fell in love and, for a time, Professor Xavier lived on Chandilar, the Shi'ar throneworld, as Lilandra's consort.
Prof. Xavier returned to Earth and resumed his position at the school. Professor X then located Kitty Pryde with Cerebro. Professor Xavier and three of the X-Men, Colossus, Storm, and Wolverine, set out for Deerfield, Illinois to contact her and possibly recruit her as a member of the X-Men. Unknown to Prof. Xavier, the mercenary, Warhawk, had planted a device that enabled his employers in the Inner Circle of the Hellfire Club to monitor Cerebro's activities. The Inner Circle, thus, also learned about Kitty, and one of its leaders, Emma, now the White Queen, also went to contact her. The X-Men then went on to battle the Hellfire Club while attempting to recruit Dazzler. When trying to understand the motives of the Hellfire Club, Angel set-up an invite to a Hellfire Club party, where the Phoenix fell under Mastermind and the Hellfire Club's control and transformed into the Black Queen. After the X-Men battled the Hellfire Club's Inner Circle, Phoenix underwent another transformation into the Dark Phoenix and soared through the universe, where she devoured an entire star and the five billion inhabitants of one of its planets. When Phoenix returned to Earth, she threatened to kill everyone, but Professor X was able to keep Phoenix under control and helped her will herself back to normal. The X-Men were then teleported away by the Shi'ar. The Shi'ar Empire had witnessed Dark Phoenix consuming the star and Prof. Xavier had no other choice but to challenge the Shi'ar Imperial Guard to a duel over the fate of the Phoenix. The battle triggered her transformation into Dark Phoenix once more and she understood that she would never be able to fully control the dark hunger inside and sacrificed herself on the Moon. Jean Grey was believed dead.
The team went on to battle the Sentinels and during a coupe, first met the alien Brood and battled Deathbird and Admiral Samedar to restore Lilandra to the Shi'ar throne, where Prof. Xavier was sent into a coma. Unknown to anyone, Professor X had been implanted with a Brood Queen egg at the time. Professor X woke from his coma to learn that his X-Men and Lilandra had left him. Around this time, Professor X aided Spider-Man in battling Mentallo and was unable to rebuild Anthony Power's son, Matthew's, comatose mind. Professor Xavier was able to help Dr. Lykos, who had been trapped as Sauron. Professor X found that Dr. Lykos was infected with a genetic virus that mutated him and isolated the alien element in his DNA matrix, which cured him.
After a call from Reed Richards about a powerful, young mutant who's powers were out of control and encouragement by Dr. MacTaggert, Prof. Xavier took Xi'an Coy Manh to his mansion and Dr. MacTaggert, also, brought her foster daughter, Rahne Sinclair.
Donald Pierce was determined to kill Prof. Xavier, as well as other superhuman mutants and had Danielle Moonstar's grandfather, Black Eagle, murdered. Prof. Xavier and the girls went to Moonstar's aid. After Dani joined the group they went-on to rescue Roberto da Costa and Samuel Guthrie. After being captured by Pierce the youths rescued Professor X and he decided to take on a new class of mutant students whom he aptly named the New Mutants. Professor Xavier also employed a small staff to help with the raising of the students, beginning with the human Stevie Hunter, and Xi'an, as the school's secretary. Professor Xavier initially had brought the team together to use as embryos as Brood Queen was slightly influencing him.
After mysteriously trapping Psyche in the Danger Room, Professor X used her powers to attack the New Mutants. The X-Men returned from space with the knowledge that Professor X had been infected with an embryo and the Brood Queen revealed herself by transforming him. The mind of Professor Xavier asserted long enough to ask Cyclops to kill him but Cyclops declined. Dr. MacTaggert and the X-Men's space-faring allies, the Starjammers, saved Prof. Xavier by transferring his mind into a newly cloned, somewhat younger body in which his legs functioned. The experience made Professor Xavier feel like a "whole man", but his legs were having trouble working.
After Professor X had a televised debate, with Reverend William Stryker, he, Scott, and Ororo were kidnapped by the Purifiers. While in captivity, Professor X was hooked to a machine operated by Dr. Phillip Ramsey, attempting to turn him against mutants with illusions of the X-Men killing him and Reverend Stryker saving him. After Professor X was brainwashed, he fired mental bolts at Scott and Ororo, seemingly killing them, and Stryker had him taken to Madison Square Garden, where he was attached to a machine that, using his brainpower, would kill all living mutants. Magneto, with his psi-shielded helmet, was able to distract the Professor enough for the X-Men to destroy the machine. Later at the mansion, Professor admitted that Magneto was right and began to accept his offer to join, until Scott stopped him and stated that he believed in the Professor's dream and will see it come true. Professor X declined his offer and Magneto left, calling them fools.
At the return of the X-Men, Professor Xavier, initially, demoted Kitty Pryde (Sprite), to the New Mutants, an act that enraged her, until Kitty impressed him by defeating two Sidri, with the help of Lockheed. While attending a fair the New Mutants were attacked by Viper and the Silver Samurai and Psyche was kidnapped. Professor Xavier decided to aid Team America and the New Mutants left without his permission to save Dani. Xi'an was lost to the New Mutants to an explosion. Sensing the Shadow King in Xi'an's disappearance, Professor Xavier ordered the New Mutants to a vacation.
Rogue came to Professor Xavier asking for help with her multiple personalities. Professor Xavier accepted her into his school and the X-Men, even after all the X-Men and Binary stated they would quit if she was admitted, and the team reluctantly agreed. Professor Xavier and Lilandra continuously tried to understand why he felt intense pain every time he would attempt to walk and she stated that she would soon have to leave to stop her sister from starting war in her kingdom. After battling Mastermind again Professor Xavier hosted Cyclops' first marriage to Madelyne Pryor at his mansion home.
Professor Xavier, later, bid farewell to his love, Lilandra, as she returned to Shi'ar space with the Starjammers and the X-Men battled the Brotherhood, as Mystique attempted to “rescue” Rogue from the X-Men, thinking Prof. Xavier forced her leave from the Brotherhood, only to have Rogue tell her that she joined of her own freewill. Professor Xavier shocked everyone with the full use of his legs.
Professor Xavier maintained his principal of never rejecting a troubled soul and, after rescuing Rachel Summers from Selene, Professor X scanned her and welcomed her to his school and the X-Men. After the New Mutants battled a Demon Bear, Professor X invited Sharon Friedlander and Tom Corsi, two more humans, to work at his school. After returning to a ruined home, Professor X allowed Warlock to join the New Mutants.
At this time, Professor X took a visiting professorship in genetics at Columbia University, where he was beaten by a hate crime driven, anti-mutant group of students, and Professor X was slightly healed by the Morlock Healer. Professor X and the X-Men, next, battled Thunderbird, brother to the original Thunderbird and blaming Prof. Xavier for his brother's death, and the Hellions to rescue Banshee. Professor X, eventually, convinced Thunderbird that his brother died a hero's death and he released them, stating Professor Xavier was an honorable man. To rescue Banshee, the X-Men had to infiltrate the NORAD, North American Aerospace Defense Command, and the X-Men were officially outlawed. After repeated assaults, from publicly announcing she was a mutant, Dazzler returned to Professor X and asked for training in the Danger Room. After her training, Professor X provided her with a new uniform that amplified and gave precision to her powers.
Professor X met with his former lover, Gabrielle, on Muir Island and discovered that he was her teenage son's father. The autistic boy, David Haller, suffered from multiple personality disorder and had vast psionic powers beyond his father. After helping him and the New Mutants to escape from David's mind Professor Xavier promised he would always be there for him.
Feeling the return of the Beyonder, Magneto once again joined forces with the X-Men. This time, due to Prof. Xavier's weakened state from being attacked by the group of mutant haters, the Professor asked Magneto to temporarily join the team. After stopping a scheme of Loki's, Magneto went on trial in front of the World Court, and was attacked by Fenris, Andreas and Andrea von Strucker, the children of Baron von Strucker. Professor Xavier suffered physical injuries and psychic strains that left him on the brink of death and asked Magneto to become his successor as headmaster of the Xavier School for Gifted Youngsters and as mentor of the New Mutants. Lilandra and the Starjammers returned and took Professor Xavier into outer space, where they used Shi'ar technology to restore him to health, but due to damage sustained by their ship, were not able to return him.
While on the run from the Shi'ar, Professor Xavier was reunited with Illyana. Illyana had been attacked by the Magus, lost her teammates, and battled all the demons of Limbo, who had been infected with the Transmode Virus. Prof. Xavier was Illyana's last thought and she was sent to the planet that he was on with the Starjammers and, with the Professor, Lilandra, and Binary, she returned to Limbo. After defeating S'ym, they gathered all of her teammates throughout time and space and returned to the planet that the Professor was on with the Starjammers and Cypher and Warlock re-wrote the Magus' DNA, effectively reducing him to infancy. During this time, Professor Xavier scanned his students for current affairs and learned of the Marauders, the loss of Nightcrawler, Colossus, and Shadowcat, and the fact that his original students were the mutant hunting team of X-Factor. Professor X, initially, decided to return, but, later decided to stay-on and continue to aid the Starjammers, who he believed he owed his life to, and used Karma to mentally control Illyana into sending the New Mutants back home.
Muir Island Saga
After an extended sojourn in space with the Starjammers, Xavier finally returned to Earth. Both the original and second teams of X-Men reassembled under his leadership, along with new recruits like Gambit and Jubilee. Xavier led the X-Men against the Shadow King, only to have his spine broken in the Astral Plane battling his son, leaving him crippled and confined to a wheelchair once more.
While holding a mutant rights speech, Xavier was nearly assassinated by Stryfe, being infected with a fatal Techno-Organic Virus, but was saved by none other than Apocalypse. As a temporary side-effect he gained full use of his legs and devoted his precious time to the youngest recruit on his team, Jubilee.
Since the X-Men were all now highly trained adults, Xavier renamed the school in his mansion the Xavier Institute for Higher Learning. He took control of a private school, the Massachusetts Academy, and made it the new School for Gifted Youngsters, where yet another new class of young mutants, Generation X, was taught.
In a battle with Magneto, Xavier lost his temper over his old friend ripping the adamantium from Wolverine's body and used his mental powers to shut down Magneto's conscious mind by transferring it into his own. In the process Xavier's mind was inadvertently infected by the evil within Magneto's psyche. The result was that the dark sides of Magneto's and Xavier's minds combined and physically manifested themselves as the nearly invincible entity called Onslaught, who usurped Xavier's psionic powers. America's greatest super heroes narrowly defeated Onslaught, who appeared to perish. However, to ensure that Xavier never again spawned a being like Onslaught, Dr. Valerie Cooper of the United States government took him into custody. Although Xavier was willing to serve as a prisoner of the United States government, he was appalled when it turned him over to the custody of Bastion, head of the anti-mutant Operation: Zero Tolerance.
Xavier was eventually freed and found by Cerebro. He briefly led the Brotherhood during this time. He then left Earth to train a group of mutant Skrulls called Cadre K.
When Mystique blew up Moira MacTaggert's laboratory complex, fatally wounding her, Charles went to the Astral Plane to meet with her and retrieve information on the cure to the Legacy Virus, but after gathering the information he did not want to leave her alone. If not for Jean pulling him back, the professor would have died with his first love, who stated she had no regrets.
After the Legacy Virus was cured, Magneto assembled an army on Genosha. Xavier went to try and dissuade him, but it took an interim X-Men team to stop Magneto, who had crucified Xavier in Magda Square, and former lover and disenchanted Acolyte Amelia Voght to free him.
Xavier regathered his X-Men as a public team and created the X-Corp in light of the incidents with Cassandra Nova Xavier, his 'evil twin.' She had revealed his mutation to the world, something he needed to do but did not want to sully his reputation over.
In the wake of Cassandra Nova's attack on the Shi'ar, Lilandra had gone insane and tried to assassinate Charles on a trip to the X-Corporation branch in Mumbai. Lilandra, believing that too much disaster had come from the Shi'ar's involvement with the X-Men, annulled her marriage to Xavier.
Stepbrother Juggernaut defected to the X-Men once Xavier reached out to him while he had nowhere to go. Cain redeemed himself, and the brothers came to understand one another.
Shortly thereafter, Kuan-Yin Xorn seemed to reveal himself as Magneto. However, Xavier was apparently aware that the real Magneto was still on Genosha. Traveling there, he tried to start a rebuilding effort with several other mutants.
When Magneto brought the comatose Scarlet Witch, he also began to try to help her. Xavier briefly returned to help Cyclops's team with Danger, whom he revealed was a sentient entity kept in the Danger Room to help make it a unique and realistic training setting.
After mutant Layla Miller restored the memories of some of the X-Men and Avengers, they headed to Genosha where they discovered that Magneto erected a memorial garden for Xavier commemorating his death. They were horrified until Cloak faded into the grave and discovered there was no body inside. After a battle, Scarlet Witch again used her powers to restore reality and, as a slight against her father, caused 91.4 percent of mutants to lose their powers, leaving the mutant race on the brink of extinction. With reality restored, Xavier was still missing and the X-Men were unable to detect him with Cerebra.
The truth about Xavier sending Moira's students to Krakoa all those years ago was finally discovered when an energy-mass comprised of all the mutants' powers revived Kid Vulcan, now known simply as Vulcan, and in a rage he attacked the X-Men, causing Xavier to come out of hiding; his legs had been restored to him after the House of M, though he was no longer a mutant. Vulcan made Xavier tell the X-Men what he had done. After Vulcan was defeated and flew off into space, Cyclops told Xavier that he was no longer wanted at the X-Mansion for what he did, though some of the other students were more forgiving, including Beast.
Even though Xavier was no longer welcome at the Institute, he nevertheless formed a new team composed of Darwin, Havok, Marvel Girl, Nightcrawler, Warpath and Polaris for the express purpose of tracking down Vulcan before he could enact his vengeance against the Shi'ar Empire. In the midst of a coup involving Vulcan and the Shi'ar royal family, Xavier was imprisoned and briefly tortured, and then was set to be thrown into the M'Kraan Crystal. After he was rescued, Professor Xavier regained consciousness and discovered that the M'Kraan Crystal had restored his mutation, and he now maintained both his telepathy and his ability to walk. He then began a search for his old colleague Magneto.
His membership in the Illuminati gave him torment when the Hulk came for revenge and he was made steward of the Infinity Mind Gem.
His relationship with the X-Men became even more strained when Professor X tried to get involved with the first new mutant baby since M-Day, but Cyclops refused his help. Understanding he had to act on his own, Xavier helped Cable secure the baby and find an escape route. After the final battle had taken place with bloodshed and Cable jumping into the future with the baby, Bishop fired a shot to kill Cable, but instead it hit Xavier in the head.
Xavier survived the bullet impact due to the intervention of the Brotherhood and Exodus directly, though he suffered lingering damages to his mind and memories, while his telepathic abilities seemed unaffected. Despite Xavier's limits, he was trying to rebuild himself and his connections. Some were no longer as trusting of Xavier as before, including Scott Summers, though Wolverine had sought out Xavier to help him free his son from the Hellfire Club's designs.
After convincing Exodus to disband the Acolytes, he was approached by Norman Osborn for unknown purposes. Following their encounter, Xavier was taken to H.A.M.M.E.R.'s West Coast base, a restructured Alcatraz Island and slowly stripped of his telepathic powers through the machinations of Dark Beast. Eventually joined by Beast, who had been arrested during a riot, he attempted to convince him that he was the real Xavier in order to warn him.
Meanwhile Osborn recruited Mystique to impersonate Xavier in public. During the Dark Avengers' arrival in San Francisco to enforce martial law and squelch the anti-mutant riots occurring in the city, Mystique, posing as Xavier, publicly denounced Cyclops' actions and urged him to turn himself in. Emma Frost managed to detect the real Professor X, later helping Emma to enter the Sentry's mind. However, after Emma worked to free the Sentry of the Void's influence, a minute sliver of the entity itself remained in her mind. Xavier quickly told her to remain in her diamond armor state to prevent the Void from gaining access to her psi-powers.
After Legion regained consciousness from his creation of the Age of X universe, Charles together with a team of X-Men helped him find his lost personalities. After Legion suffered a massive shock to his nervous system, Charles vowed to take care of him and nurse him back to health.
Avengers vs X-Men - Death of a Mentor
Charles was seen on the shores of Utopia with his son in intense pain together with various other psychics as the Phoenix arrived to choose its host, which ended up being five X-Men. Later, after the battle of Wakanda, Charles telepathically contacted Scott Summers to express his severe disappointment in their recent actions and made it clear that unless they ended their madness right away, he would have to take action and use the appropriate actions to bring the X-Men down.
After the power of the Phoenix was only distributed between Scott and Emma Frost, Charles aided the Avengers to take them down. His powers managed to nullify Scott's for a small period of time in which the Avengers attacked. Knowing he couldn't defeat the Avengers without the whole Phoenix Force, Scott took the final portion from Emma. Xavier attacked again and demanded he stop but Cyclops finally lost control and somehow killed Xavier before turning into Dark Phoenix.
Charles's death caused a mental shock wave that caused Charles son, David Haller a.k.a Legion to lose his control over his powers and birth a new persona that at first took the shape of a yellow goblin-like creature and later the form of Charles Xavier himself. David also made it his mission to uphold his father's legacy
After his death, Charles Xavier's brain was harvested by the Red Skull, who took Xavier's vast psionic powers for himself.
As part of his last will and testament, Xavier left his Infinity Gem to Beast, leading to Beast being inducted into the Illuminati as Charles' replacement.