Jonathan Xavier AKA Professor X 2099 was a clone and reincarnation of the original Professor X.
The original Charles Xavier had been dead a long time. He was always remembered though, for his wisdom and bravery. In 2099 the city was in chaos because of crooks and supervillains, so scientists had advanced technology that could clone the long dead Professor X. They created a clone and genetic reincarnation of the original Professor X, resembling the original Professor X in his 20's. He had all the powers as well as the personality as the original Professor X. The scientists who created him wanted to experiment on him, frightened he escaped the laboratory and used the wealth he had inherited from the past Professor X to rebuild the deserted, old, about to collapse mansion of the old Charles Xavier with the help of descendants of the old Professor X's workers. He named himself Jonathan Xavier and adopted the superhero alias Professor X.
Fight with Magneto 2099
Howard Graham a young salesman discovered he had the power to control magnets. Howard was a self centered evil man so he decided to wreak havoc. He called himself Magneto 2099 because of the original Magneto and designed his own suit to look like the old Magneto's suit. As Magneto 2099 wreaked havoc on New York city, Professor X 2099 decided to stop him. He had a fight with Magneto 2099 at an old abandoned chocolate factory in downtown Manhattan. They fought a long intense battle but however, in the end Professor X's mind games and telekinesis powers along with his martial arts skills were strong enough to beat Magneto 2099! But in the end he accidentally killed Magneto 2099 by accidentally pushing him into a bottomless vat where chemicals had been in the old days.
Meeting Spiderman 2099
When the green goblin 2099 terrorized the city, Professor X 2099 teamed up with Spiderman 2099 to stop him. They defeated the green goblin 2099 and since that they've been good allies.
Return of Magneto 2099
Magneto 2099 wasn't really dead and had survived the fall in the chocolate factory. He wanted revenge against Professor X 2099. So he met Mystique 2099 a male descendant of the original Mystique and started attacking the city and killing people which made Professor X 2099 angry. So Professor X 2099 fought them but couldn't defeat them. So he teamed up with Goliath a descendant of the blob that was a good guy. With their combined powers and their minds they defeated Magneto 2099 and Mystique 2099 and put them in jail. The time Magneto 2099 and Mystique 2099 were in jail made them want revenge more and more.
Being a fugitive
In an alternate universe there was an evil Professor X 2099, called Chaos Professor X. He traveled to his universe and framed him for murder. So everyone was after Professor X 2099 thinking he had done the crimes. So he became a fugitive and lived in Texas under the alias Jethro Jones and had a job as a sheriff. Chaos Professor X was looking for him. For months and weeks Jonathan Xavier AKA Professor X 2099 lived in Texas as Jethro Jones keeping a low profile. But eventually Chaos Professor X came to Texas and discovered him. They fought each other and when he defeated Chaos Professor X people realized he hadn't commited the crimes so he moved back to his mansion in New York city not a wanted man anymore.
Fight with Dr. Doom 2099
Eventually Dr. Doom 2099 would come to New York city. Dr. Doom 2099 had a disfigured face he hid behind his mask, at a chemical factory a chemical that could cure his face was being used by workers. But it was expensive. Dr. Doom 2099 didn't have the money so he decided to steal it because the workers wouldn't give it to him. But Professor X 2099 however would thwart his plan. So then Professor X 2099 made enemies with Dr. Doom 2099 by putting him in jail and stopping him. Dr. Doom 2099 would later return for revenge trying to steal Jonathan Xavier's wealth to buy the chemical but Professor X 2099 discovered this and fought him. Dr. Doom had grown stronger so the Professor couldn't defeat him but then Professor X used his mind powers to defeat him.
After defeating Magneto and all those villains Professor X 2099 was a hero but people would still treat him like he was a monster because he was a mutant and in 2099 not much had changed. A man named Joshua Horowitz formed a group of people that hated mutants. They called their selves W.D.W.M. (stands for We Don't Want Mutants). W.D.W.M. wanted to kill Professor X just because he was a mutant. They formed an angry mob and attacked his mansion. The Professor didn't want to fight them so he communicated telepathically that he didn't want to hurt them and that mutants weren't a threat but then they refused to listen and tried to attack him. He used his mind powers to confuse them and wipe their memories so they forgot about their meaningless hatred for mutants and they lived normal lives without hating on mutants. Magneto 2099 and Mystique 2099 broke out of jail and convinced the former members of W.D.W.M. to have a reason to attack Jonathan Xavier so they made an attempt to attack the mansion again. Magneto 2099 and Mystique 2099 helped them. Professor X 2099 used his powers to wipe their memories again and the cruel Magneto killed the members of W.D.W.M. so Professor X 2099 thought that what Magneto had done was evil so he fought him. Mystique 2099 shape shifted into Magneto 2099 to confuse Professor X so then they fought a long intense battle and the Professor had no idea which one of them was the real Magneto 2099. But however in the end he used his wits to defeat both of them. They were then sent back to jail. But then they were freed by the evil version of Professor X known as Chaos Professor X who had returned. After Professor X 2099 had used his powers to stop a bank robbery Magneto 2099, Chaos Professor X, and Mystique 2099 confronted him. He was outnumbered by them and not even his mind powers could stop them. But with the help of his old friend Spiderman 2099 and Goliath he defeated them. Mystique 2099 fled from the battle and Magneto 2099 even though he was injured by their attacks got up and still fought. But Chaos Professor X and Magneto 2099 both were defeated. But they didn't give up so they used their powers to merge and they became Onslaught 2099. Professor X 2099 and his superhero friends were no match for Onslaught 2099. He was too powerful and he had Magneto 2099's power to control metal and Chaos Professor X's mind powers, both their powers combined! In the end they figured out that Onslaught's armored helmet (resembling Magneto 2099's helmet) had a mind barrier blocking Professor X 2099 from using his mind powers. So Goliath and Spiderman 2099 distracted him and took his helmet and Professor X 2099 defeated him with the power of his mind. Eventually Onslaught 2099 would return seeking revenge. Doctor Strange 2099 (the future doctor strange that's a woman) allied with Professor X 2099 because Onslaught 2099 had also been a foe to her. They fought Onslaught 2099 in an intense battle but Onslaught 2099 would eventually defeat them. Professor X 2099 and Doctor Strange 2099 would be comatose for a while. When they awoke Onslaught 2099 had created his own planet Asteroid M and he wanted them to join him and be evil. Aliens were allied with Onslaught 2099 and when they refused to join the evil being the aliens attacked them. But the aliens were defeated and Onslaught 2099 was trapped in another dimension by Doctor Strange 2099. Doctor Strange 2099 and Professor X 2099 then returned to Earth. Eventually Professor X 2099 faced an energy entity Phoenix force and sadly was killed. He couldn't come back because as a clone was made of dead cells. But eventually he was somehow revived and defeated phoenix force. Mister Sinister 2099 a man possessed by the original Mister Sinister trapped Professor X 2099 inside another dimension and tortured him thinking he was the original Professor X. During the time he tortured Professor X 2099 the original Professor X's persona briefly returned from within Professor X 2099 telling Mister Sinister "STOP THIS MADNESS BEFORE IT'S TOO LATE MISTER SINISTER!!!!" but instantly reverted into Professor X 2099. Why this happened is unknown. But Mister Sinister attacking him probably alerted the original Professor X who was within him and he took control over the future Professor X and tried to communicate with Mister Sinister. Eventually Professor X 2099 used his mind to defeat Mister Sinister 2099 and return to his dimension.