Early Life[]
Charles Francis Xavier was born in New York City. With the small fortune, he had inherited from his mother, Charles turned his family's mansion into his Xavier's School for Gifted Youngsters, in the hope of helping young mutants learn to control their powers. Ororo and Logan became instructors at his school and took the code names Storm and Wolverine. Using his powerful mutant-tracking computer, Cerebro, Charles sought out his first two students, Scott Summers, who possessed optic blasts, and Jean Grey, with mental powers similar to the Professors'. Eventually "Professor X" recruited others, and the fledgling X-Men were born.
Season 1[]
Professor X trained the X-Men to control their abilities and to use them against those who would harm others, such as The Brotherhood. He guides his students sternly, but with a fatherly love that binds the entire team together. Recently, Professor X brought a number of new students to the school and recruited a new teacher, the Beast, a Bayville alum who had previously turned down an offer to join Xavier's cause. All together, Professor X and his staff run the Xavier Institute as a supplementary program for the students, who all attend Bayville High for their regular classes.
Following the explosion and the authorities arrival, in a nearby limousine, Charles Xavier arrived on the scene in time and successfully was able to purge the mind of a policeman whom caught suspicion that it was more than a leak in the propane tank. Satisfied, Charles tells the driver that they have a train to catch. At the previously said subway station, Ororo Munroe accompanies Xavier, where he planned to meet Kurt Wagner]. Ororo asked Xavier if any of the passing people were him before Xavier told her they were not, setting his sights on the real Kurt who's dressed in overcoats.

At the Xavier's School for Gifted Youngsters, the next day, Scott was rushing Jean out of the bathroom claiming that they were going to be late for high school while she was brushing her hair. Jean told him to hold on for a second and that she was almost done. Scott exclaims that he was going to blast the door down before Jean comes out. She teasingly asking him if they were going or not, sliding a finger along his chin before walking off. As she and Scott prepared to leave, the two were halted by Xavier, whom stated that it would be just for a moment. Once they were in the study, Xavier introduces them to Kurt Wagner. At first, Kurt was very shy but Xavier reassured him that he was among friends. After Scott tried to give him a handshake, Jean and Scott both expressed shock in the appearance of Kurt's blue three fingered hand.

Xavier then began to discuss Scott's mistake by scowling him for using his powers in such a manner the previous night and that he must be more careful. Scott rhetorically asked what his mentor expected of him to do with such tremendous abilities. Xavier explained that he wanted all his young students to have better control and explained Scott's powers to Kurt. He claims that Scott's powers are cool as Kurt removes his hood. Jean then asks him what his special gift was as he demonstrates by teleporting across the room, impressing both Jean and Scott. Xavier tells them that Kurt will be settling in and that they will talk more tonight.

Sometime later, Xavier and Ororo show Kurt to his room. As Kurt is surprised that he gets his own room, Xavier states that his parents sent him to the Xavier Institute because they knew he would be happy here. Kurt questions how can he be happy when he has his demon appearance, further stating that he scares people. Xavier tells Kurt that he has a surprise for him as he gives Kurt an Image Inducer, allowing him to receive a human appearance. In his delight, Kurt exclaimed that Xavier had made him normal followed by Ororo citing that he was already normal and he didn't need the accessory to be that. However, Xavier explained that the device could only project an alternate appearance of a human and that he still had his blue and furry form. Kurt tells Xavier that he understands but was still pleased to have the device and even more so when he saw his X-Men uniform.

Cerebro detects mutant signature.
Later that day, Xavier noticed that Cerebro has detected a recent mutant signature before he was contacted by Scott via phone about his classmate, Todd Tolansky. Scott expressed distaste in Xavier recruiting him as Scott cited that Todd has the personal hygiene of a dead pig. However, Xavier tells Scott that the X-Men do not turn their backs on anybody. Scott asks his mentor if he should invite Todd to the institute but Xavier tells Scott there's no need. Nightcrawler arrives and asks Xavier what Cerebro was, as the former explains that Cerebro detects the manifestations of mutant powers like how he found Kurt. Xavier then contacts Ororo via telepathy and asks if she would "audition" someone for him. After Toad's test, Xavier says that he could be one of them as Storm claims that she believes that sometimes even his good heart blinded him from the truth. As Toad and Nightcrawler continue chasing each other and wrecking the mansion, Xavier announces that Toad has passed the test and would be allowed to join the X-Men if he so desires. But Toad does not want to join the X-Men as he still proceeds to attack Nightcrawler. The two quickly were at each other's throats before Nightcrawler teleports himself and Toad into the Danger Room where they were attacked by the room's automated defenses. Xavier contacts Jean Grey and Cyclops telepathically while ordering them to get Nightcrawler and Toad out of the Danger Room.

Charles welcomes Logan home.
After Cyclops and Jean save Nightcrawler and Toad, the latter is terrified by the X-Men's protocols and decides to leave. Cyclops tries to stop Toad from leaving but he was too injured to catch him. Xavier says that Toad was not yet ready to be an X-Man. After being saved and seeing Toad depart, Nightcrawler's upset about causing the accident as he begins to doubt himself about him not being ready to be an X-Man. He further tells Xavier that he does not belong here as he teleports away. Cyclops goes off to convince Nightcrawler to stay with the X-Men.
As Toad was prepared to depart from the X-Men's residence after being horrified by their protocols, he encounters Wolverine. As Toad cowers, Logan was more than ready to attack him but Xavier urged him not to as Toad held no real threat after which Logan gave Toad the courtesy of leaving without confrontation. Once Toad was gone, Logan told Charles that he came back because he smelled trouble before noting that it may have just been Toad. Charles welcomes him back as Logan tips his hat as he smiles back at him.
At the school, the Kityy Pryde's mutant signature is picked up by Cerebro as it gives Charles Xavier her statistics, she is fifteen, who lives in Northbrook, Illinois. Xavier tells someone to prepare the Blackbird.

Jean with Xavier to talk to Kitty's parents
Later, Jean was selected by Xavier to accompany him in the recruiting of Kitty. While traveling in the Blackbird, Jean questions why she was chosen for aiding him and not the rest of the team before Xavier explains that she could connect with the girl. Jean then asks about the other mutant signature that Cerebro picked up, the one in the foster home. Xavier clarifies the mutant's name is Lance Alvers as he tells her to keep her focus on Kitty and her parents and to let him worry about Lance. The two arrived at the girl's home, where her father rudely tells them that it's none of their business and to leave them alone as he profoundly slams the door in their faces. Jean cited that next time, they should call and get hung up on instead before Xavier explains that she would have to make direct contact with Kitty at her school.

Soon afterward, Jean contacts Xavier via cell phone while he's at the Social Services Building in Chicago. She tells him about Lance's reaching out to Kitty while Xavier concludes that if Lance does then they won't be able to reach her. Jean agrees as Xavier tells her that he doesn't want to lose her and to stay with it and to keep trying. Awhile later, outside of Kitty's school, Jean Grey and Xavier met up with Kitty's parents telling them that Kitty has broken into the office as her parents tell them that she has never done something like this before. Jean departs with Kitty's parents to go find her as Xavier tells them that he'll catch up.
Things eventually escalate to the point where Lance decides to bring the whole school down to stop Kitty's parents and Jean from following them. Jean manages to use her telekinesis to keep the ceiling debris from collapsing around her and Kitty's parents with Xavier's psychic help. After using her powers to save her family, Jean and herself, Xavier tells Kitty that she used her gift well. Kitty hugs and apologizes to her parents as she tells her father that the X-Men want to help her and that she trusts them. Her father agrees as they all decide to talk with Professor Xavier about Kitty entering his school.

Xavier scowls Nightcrawler for frightening Shadowcat.
At the Xavier Institute, a ninja sneaks into the mansion before being attacked by Storm in the Danger Room. He manages to dodge her initial attacks and strategies to get him before he lunges at her and is frozen. While breaking out of his frosty confinement, revealing the ninja is Wolverine tells her that what she did to him was cold. Wolverine begins to tear apart her next few deployed machines, before being stopped by Xavier, who reasons that at the moment it is the most they can afford. Wolverine adds that when he gives a demonstration, he gives a demonstration. Soon afterward, Xavier comes and tells Scott to assemble the full team. He explains that Cerebro had detected a new mutant, of whom is Rogue and he believes to be a danger to herself and others. He tells the group that they are dealing with a rogue. While the X-Men are in the Blackbird, Scott compliments Kurt on his piloting skills just as Xavier compliments on Scott's skills. Nightcrawler, who overhears Shadowcat's and Jean Grey's later conversation about Cyclops, teleports to the front of the Blackbird, in an attempt to impress Shadowcat. However, he loses his footing and begins to fall, teleporting into the Blackbird and falling on Shadowcat. After scolding from Xavier, whom reminded him that he had frightened her, Nightcrawler apologizes. However, Shadowcat tells Nightcrawler to stay away from her and walks away to sit in the front with Cyclops.

Can't read Rogue's mind...
Once the X-Men arrive, the team tries to extract information from Cody Robbins, which Wolverine questions if it's really necessary to do so. Charles relates that Cody holds the secret to their rogue. Sometime later, Shadowcat concludes that she can contact Charles with her mind and does just that, being told by Charles to calm down and lower her volume. After Shadowcat relates to Xavier that Nightcrawler is injured and Charles relates the same information to the X-Men, Wolverine blames himself and states that he should have gone with them. Charles tells Jean, Cyclops and Storm to follow Rogue and that he will guide them.
After Rogue teleports away and Cyclops and Jean saved Storm from being electrocuted, the former asks the arriving Charles what happened to Rogue. Charles tells her that she has teleported away and that he cannot detect her before relating that he senses the work of another person in their attempts to recruit Rogue. Wolverine sniffs and smells Mystique, stating that she can change her appearance, but not her scent. After Shadowcat tells them that they have to go after her, Charles tells her that they have had enough damage and Rogue must come of her own free will or not at all, also noting that they must tend to their wounded as they return home.

I know stuff!
Xavier contacts Storm and tells her Jean and Scott are coming to help. He also tells Storm that Cerebro picked up another mutant at the ball game. Xavier will use his influence to get Evan out of jail if Evan will join the school.
At the mansion, the X-Men are hanging out in the pool. Kurt cannonballs in and knocks Kitty off of her float. Xavier talks to Evan about how they're happy to have him. Evan jumps in the pool, lands on Kitty's float and pops it with his spikes. Xavier tells Storm that Evan fits in just fine.

Owned! by Magneto!
Scott freaks out and stops the simulation. The base disappears and Rogue shuts down and drops to the floor. Charles Xavier comes through Danger Room doors and tells Scott that he's never to stop simulation unless he's hurt. Scott tells Xavier that Rogue was not supposed to be part of the simulation. Xavier said he added her as an element of surprise and that they have to get used to that during missions. He tells them the training session is over and it's time to go to school. At the mansion, Xavier's confronted by Magneto. Magneto tells him that his kids are doing well but that Xavier does not trust them with the truth. He slams Xavier into the glass doors.

WTF! Jean can't go?!
At the institute, Xavier, and Logan talk about the kids not knowing that Darkholme is really Mystique. Logan says they should tell them the truth, but Xavier says he doesn't know if they're ready for it. Storm and Jean walk in, saying that there is trouble brewing on the mountain, a blizzard's coming in. Xavier asks why Jean isn't with them, and she tells them how Darkholme pulled her to make room for Rogue. Xavier, Wolverine, and Storm fly towards the mountains in the Blackbird on their way to find Scott. Xavier tries to contact Scott telepathically and then tells Storm and Logan that he's hurt. They're worried that they won't be able to find him in the white out of the blizzard.

Yo! here' the deal!
A beam blasts through the snow and the X-Men follow it. X-Jet arrives and Mystique flies off. They pick up Scott and Rogue as the bridge collapses.
At the institute, the kids confront Xavier about withholding info about Mystique who is their principal. Xavier asks Rogue what she thinks. When Rogue says it isn't her place, Kitty tells her she's part of the family now. Rogue tells them that she's found that honesty is very important. Xavier tells them he'll try to be more open with them in the future.
Sabretooth rips open the front gates of the school. The rest of the X-Men come running. Wolverine tries to keep them out of it but Storm tells him it's no place for his personal wars. Through a combined effort they send Sabretooth packing on his way again.
Logan talks to Xavier about Sabretooth coming after him and that he'll probably try baiting Wolverine away from the school. Xavier realizes this means he'll try to take one of the students, and that they're all in danger now.

They drop Sabretooth off in the snow (Alaska) and Xavier wipes his mind.
The high school shows Spyke's "film" at the end about the X-Men being his new family. Each of the X-Men are shown in some candid shots and the last shots are of Kitty and Rogue both dancing in the school play together and Spyke dedicating it to his new family. All the other X-men show up to support him. They smile at the end to each other.

At the Xavier Institute, Charles Xavier is keeping track of the X-Kids with Cerebro. Logan asks if Xavier told them not to use their powers. Xavier tells him that he had hoped they'd use their own judgment and decide not to. Wolverine says that he should have taken care of their survival training himself, and Xavier tells him that the kids felt they had a better chance of surviving the camp.
Cerebro picks up a signature and Xavier finds out that it's Juggernaut on the loose. Xavier explains to Wolverine that Juggernaut is Cain Marko, Xavier's half-brother, and how he used mysticism to awaken his dormant X-gene. Juggernaut is now virtually invulnerable and wants to take revenge on Xavier for having him locked away. They show Juggernaut trashing police cars.
Storm takes off in the X-Jet, she flies above the area where Juggernaut is traveling and creates a dense fog. Xavier believes that it will keep others (police, etc) from trying to catch Juggernaut and getting hurt.

Juggernaut reaches the Danger Room (where the prof is hiding) and knocks out Wolverine. Mystique comes in, yelling at Juggernaut for not holding up his end of the deal. He knocks her away and tells her that he doesn't make deals. Mystique crawls backward and is trapped with Xavier as Juggernaut advances.
At the Xavier Institute, Xavier tries to talk Juggernaut out of harming him. When Juggernaut won't listen, Xavier activates the Danger Room. Juggernaut destroys everything in his path and is about to reach Xavier when the X-Kids and The Brotherhood arrive. He reaches for Xavier, but Jean uses her telekinesis to pull him away. She can't hold him long though and collapses.
Wolverine tells them to try to get Juggernaut's helmet. Juggernaut goes for Jean, but the Blob rushes in and knocks him away from her. Nightcrawler ports in while he's stunned and unlatches one of the four latches holding on his helmet. Juggernaut throws Nightcrawler and then charges the Blob and knocks him back across the Danger Room.

Cyclops blasts him, but Juggernaut picks up a piece of the Danger room wreckage and throws it at him. Avalanche uses his tremors and is able to make him stumble. Quicksilver is able to get to him long enough to open another latch. Juggernaut throws Quicksilver off, but Storm steps up and disorients him with wind gusts. He stumbles back and falls. Kit and Rogue phase out of the wall and are able to get the last two latches. Toad uses his tongue to grab Juggernaut's helmet and yank it free. Xavier is then able to use his powers to take out Juggernaut.
As the X-Kids and Brotherhood cheer and congratulate one another, Mystique comments about it not being a sight you see everyday. Xavier agrees and Mystique takes the Brotherhood home.
Later Xavier returns Cain to prison. On the way out Jean and Scott flirt and then talk about how good it was to fight alongside the Brotherhood.

Lets take a look...
A few hours after going to sleep, Rogue wakes up screaming.Everyone rushes into the girls' bedroom to find out what's going on, and as Rogue is telling them about the nightmare, she realizes that the baby in her dream was really Kurt. Xavier asks Jean, Rogue and Nightcrawler to come down to the library where he reads Rogue's mind. The Xavier is able to see the woman's face and realizes it's Mystique. He also watches as a couple scoop Kurt out of the water and Mystique watches them from a distance and then turns and walks away. Xavier tells them that Rogue is really experiencing the repressed memories of someone that she's touched, someone that has knowledge of Kurt's past. Kurt believes that they're his memories and he wants the Xavier to read his mind and see if he can find out more about his real parents. Xavier tells them not tonight that he'll try to find out more tomorrow., but he doesn't tell any of them that it was Mystique in Rogue's dreams.

The next day at Bayville High Xavier goes to see Raven at the high school. He asks her what they were doing in the castle and about Kurt. She thinks he's bluffing, but some of the memories come back to her. Xavier asks if it was worth the loss of her son and she yells at him to get out. Before he goes, he tells her, her son has turned into a "fine young lad". As he leaves he telepathically communicates with Logan with the location of the castle and Logan takes off in the Blackbird.
Back at the mansion, Xavier tells Logan, Jean and Scott everything he knows about Mystique and Kurt and about Magneto doing genetic research. He says they may never know for sure if Mystique is really Kurt's mother, or what was done to Kurt in the lab. They decide not to tell Kurt what they've learned.

You OK, buddy?
Xavier talks to Wolverine about his intense nightmares in a courtyard. He asks to reads his mind to find out what the nightmare really is...Possibly a suppressed memories of how Logan got his Adamantium and was experimented on, and that Mt. McKenna has something to do with it. Logan gets up to leave but Xavier stops him, tells him he knows he's headed to Mt McKenna to find out what's happening there. Logan walks away as Xavier asks if he wants company, but Logan declines.

You're ok now!
Back at the mansion, Logan comes to in the med-lab. Xavier tells him that he's alright and Logan asks about the kids. Xavier tells him that they're fine and Kitty's been in every hour to check on him since the surgery. That they removed the chip. Wolverine says he's going to find out someday who had this done to him.

Logan walks into the new cerebro and Charles Xavier tells him that they've found a new mutant. When Logan asks him what the big emergency is Xavier tells him that Alex Summers is Scott's brother. Logan says he thought that he died in the plane crash and Xavier says that they all thought he did. He tells Logan to have Scott meet them in the hangar that they're going to Hawaii.
In the hangar, Xavier tells Scott about his brother being alive. Scott freaks saying he should've looked for him sooner, he shouldn't have believed he was dead. They load up into the Blackbird and leave.
In Hawaii, the Blackbird lands on the beach. Scott and Logan get out and find Alex's surfboard. They follow the footprints and Logan says that Magneto has been there. In the jet Xavier tries to telepathically talk to Magneto, the jet is suddenly pulled off the ground. Wolverine runs after it and is able to jump up onto the landing gear. Wolverine tries to climb up into the blackbird while Magneto and Xavier argue telepathically before Wolverine disappears.

The Blackbird hovers into Magneto's base in space, Asteroid M. Magneto greets Xavier and tells him that all of the X-Men are facing a "trial by fire". The X-Men and Brotherhood will fight and the winner will win sanctuary on Asteroid M. Xavier tries to talk him out of it, but Magneto won't listen. Magneto tells Xavier "it's almost over now".
Magneto asks Xavier to join him and Xavier asks him what happens to those that won't. Magneto shows him Rogue, Jean, and Storm in stasis tubes. He tells him that for everyone that he has to force, another recruit comes along willingly. Alex and Scott walk in (wearing matching outfits no less) and Xavier looks shocked and says "Scott, No!"

On Asteroid M, Xavier confronts Scott about why he's there. Scott says he's just there to listen. Xavier points to Jean, Rogue, and Ororo and asks Scott if they're just there to listen also. Scott gets angry and wants Magneto to let them out. Magneto says he's only being cautious and he'll let them out soon. Xavier tries to talk some sense into Cyclops, but Magneto puts him into stasis also. At the last minute, Xavier is able to get off a warning to Wolverine, telling him to lose the fight. Magneto brings the other X-Men out of stasis in time to see Scott enter the enhancer. Xavier tries to stop Scott, but the door slams shut as Scott tries to get out. Scott and Alex come out of the enhancer as adults (both with white hair). Magneto gives Alex the code name Havok and tells Scott he can take off his visor. Then he tells them that the enhancer has affected their minds as well, wiping out emotions.

They pick up an incoming aircraft and Magneto tries to use his powers against it. When he realizes that there's no metal for him to control he sends out Alex and Scott to "defend them" Jean and Xavier try to free the brothers, but they end up freeing themselves by blasting their way through. They argue with Jean and Xavier. Jean finally tells Scott that if he's the future, she doesn't want anything to with it. She walks away as Xavier tells Scott he just crossed the line and then leaves also.

The X-Jet comes back for Scott & Alex when they begin to run for it, but there are still too many tremors and falling debris and it can't get to them. Asteroid M begins to fall and Alex and Scott use their powers to blast it apart as it crashes towards them. They both collapse to the ground back to normal.
The X-Jet lands and Scott apologizes to everyone for the way he's been acting. Alex says so much for Havok, but at least I have my brother back. Xavier tells Alex that they'll help him with his powers if he wants and that they'll do it together, unified, as the X-Men.
Season 2[]
In Xavier's office, he and Logan are discussing the new recruits and the difficulty they will have keeping anonymous, Logan expresses his feelings that they need more instructors, and possibly a couple tanks... Storm comes in and turns on the TV, showing Xavier and Logan the news report, displaying a car being knocked away from the bus by a strange bolt of red light. Xavier automatically realizes it was done by Scott.

In front of the Academy, Scott drives up in his car, with Kurt and Kitty still in tow. The three are discussing whether or not to tell anyone what happened, and Kitty suggests either keeping quiet about it or finding a way to blame it on Kurt. They look to the front doors to see that Logan, Xavier, and Storm are already there, waiting for them.
Scott and Xavier talk in his office about hiding the fact that they're mutants. Scott wants to stop hiding the truth as he thinks that they are hiding in shame, they should be using their powers to help people. Xavier agrees that they should help others in need but he also tells Scott that mutants must remain anonymous as he doesn't think that the public is ready to embrace the fact.
At the prep game rally, Xavier is sitting with the other X-Men as Principal Kelly shows off the new high school mascot the "Bayville Hawk", which shoots off fireworks. When the game begins, The Brotherhood show up and interrupt the game as Avalanche and the others announce that they're mutants, that they have special powers. He also announces that the Xavier Institute is also filled with mutants, naming Jean and Scott personally. The Brotherhood starts wrecking the stadium and harassing Kelly. The X-Men prepare to handle the situation at hand, Xavier calls to Storm telepathically that the X-Men need her help. Storm appears and creates a rainstorm to stop the spreading fire from the Brotherhood's previous antics. Xavier thanks her but she says that the downpour won't make people forget what they have seen, that the secret of mutants is out. Xavier suggests that he alters everyone's memories of what has happened so that they would forget the exposure of mutants. Storm loudly protests saying that there are too many people even with his powers, his mind wouldn't be able to handle the strain. Xavier says that he doesn't really have a choice in the matter as he begins to wipe the people's memories, against Storm's wishes. He works his way through all of the students, but just as he's clearing Kelly's mind he loses consciousness.

Back at the X-Mansion, Xavier comes around and Ororo says that it worked. Everyone thinks that the Hawk's fireworks caused all of the damage. Xavier asks about the television coverage and Logan tells him that some weird magnetic interference stopped the broadcast. They all realize that it means Magneto is still alive somewhere. Scott tells Xavier that he knows now that the world isn't ready to find out about mutants yet. Xavier says that he hopes the Brotherhood boys would come to realize that but his main concern was Principal Kelly as Xavier doesn't know if he finished wiping Kelly's mind clean or not.

At the Xavier Institute, Xavier lectures Kurt and Tabby. He puts them both on restrictions for 2 weeks, which includes being grounded, no powers, and 2 sessions with Logan daily. Tabby is about to say something, but Kurt stops her and tells Xavier that they understand.
At the X-Institute, Xavier is telling Tabby's father that he can't see her. Her dad grabs Xavier and threatens to bring in the media and tell them all about what's going on at the Institute when Wolverine shows up. He tells her dad that he's going to remove his hands. Just then Tab and Kurt walk in.
- Day of Reckoning I and II
At the beginning of the infamous "Day of Reckoning" fiasco, Professor Xavier appeared more stern and unforgiving of his students, upset that they were unprepared to fight against Magneto. Because of this lack of training, Xavier announced to his students that they would be joined by The Brotherhood. This action upset Cyclops, who subsequently left the team. Xavier assembled the team, leaving the New Mutants at the Xavier Institute because they were inexperienced, and flew off to find Wolverine and attack Magneto, still believing that Magneto was responsible for Wolverine's disappearance. As soon as the Velocity and X-Jet were gone, the Mansion went into Defcon 4, locking Magma outside and the rest of the New Mutants inside. Moments later, Cerebro set itself for emergency demolition. When Cyclops returned, after prompting by Boom-Boom and Magma, he was able to save himself and the New Mutants at the last minute. In New York City, the battle raged between the X-Men/Brotherhood team-up and Magneto's own mutants, Sabretooth, Pyro, Colossus, Gambit, and Quicksilver who had led the teams into a trap, knowing he would be same. As the battle continued, and Magneto's team was defeated, the Sentinel, created by an anti-mutant fanatic known only as Bolivar Trask, surfaced. The battle between the X-Men/Brotherhood and the Sentinel was so massive that it devastated a decent sized area of New York, and was played around the world on television, revealing that mutants exist. After the battle was finished, the team had to flee quickly, leaving Beast, Rogue, Spyke and Blob behind. This was very uncharacteristic of Xavier. However, when the remaining team returned to the destroyed Mansion, Cyclops accused Xavier of destroying the Mansion and nearly killing him and the New Mutants then lifted him out of the chair and tossed him to the ground. The others tried to subdue Cyclops when Xavier stood up and morphed into Mystique.
Season 3[]
With news footage identifying the X-Men as Bayville students and the Xavier Institute being rebuilt, Professor X had the X-Men return to Bayville High, following a successful referendum on their status. When Mesmero resurfaced to find the second key to Apocalypse's tomb, Xavier was the one who discovered that the destruction of the second key was exactly what Mesmero wanted, as the spider was a guardian to protect against Apocalypse's return.

Eventually, thanks to information from Juggernaut's mind, Rogue led the X-Men to Professor X at Stokes County Maximum Security Facility, and the X-Men freed their mentor from Juggernaut's stasis chamber, where Mystique had stashed him.
The President gives a speech saying that the X-Men have been cleared of all charges and that the real villain behind the Sentinel fiasco, Bolivar Trask, has been jailed. He says that everyone should be more open-minded about mutants and that from now on they should be free of any prosecution.

Jubilee's parents have come to take her home. As Logan watches, he tells Xavier that first Rahne is gone, now Jubilee. Xavier tells him that he understands, and that the parents don't feel that their children are safe after all that's happened. Wolverine blames himself, saying he should’ve caught Mystique’s scent when she was there posing as the Prof., and Xavier says he should’ve sensed her in Wanda’s hospital room before she abducted him: “But the fact is, with her advanced mutant powers, she’s now able to conceal herself completely from us.” That night Jean gives a speech; as she is finishing her speech, Lance starts to bring down the entire auditorium.

Everyone rushes outside and Kelly tries to turn the board members by saying that the mutants are all out of control. That they can't be allowed back to school. Xavier says that his students are showing remarkable control, even against the overwhelming urge to use their powers.
Next morning, Xavier calls everyone to another meeting. Logan asked if they are on their way to a funeral as everyone walks by with sadden faces. He tells them that the board voted to allow them back into school. The kids aren't too happy about going back, but Xavier tells them that it's not only an honor for them to be taking the first step in this "new world", but it's also their responsibility for the mutants yet to come. He tells them how proud he is of them, and that no matter what, the X-Men will endure.
Season 4[]
When Mesmero returned to enslave Rogue, using her to absorb all of the powers of the X-Men, The Brotherhood and The Acolytes. During Jean and Scott's graduation ceremony, Magneto and his team arrived, ruining the ceremony, and allowing Magneto to tell them what Rogue had done. The two teams combined, an Xavier realized that he might know where Tomb of Apocalypse was. With the help of Cerebro, Charles unlocked the memories he gained from Mesmero and believed to have found that Apocalypse was entombed underneath Giza. However, when the combined Brotherhood/X-Men team arrived, they found out it was a trap, and fought their way through to an ancient room, where Beast translated the Hieroglyphics and found out that En Sabah Nur was the first mutant, and that an ancient pharaoh named Rama-Tut had found a ship hr believed not of this Earth, though it had really been created in the future, and that Apocalypse had seized control of it in order to turn all the world's people into mutants. Using his own mind to control the ship, Xavier teleported them all to Apocalypse's real tomb in Tibet, where Gambit, Sabretooth, and Wolverine had tracked Mesmero, Rogue, and Mystique to already. However, the team arrived too late to stop Apocalypse from drawing all of their powers from Rogue and becoming powerful enough to live up to his name

Knowing what will happen to jean...
Later, Apocalypse captured the Professor and turned him into one of his Horsemen. Outfitted with biotech weaponry and a flying horse, Xavier was able to ignore his crippled legs and fight aerial battles. The X-Men were forced to fight their mentor, with Jean providing most of the telepathic support. Eventually, they defeated Apocalypse and the Professor was returned to normal. Following the event, he appeared to have a precognitive flash of various changes that would soon occur to his students, some good and some bad...
The Future[]

Future Beast
In The Future Charles Xavier, along with many other X-Men are still at the X-Mansion in active service.