ALTERNATE VERSIONS - Page 1
In the reality depicted in What if (2nd series) #9, the all-new, all-different X-Men were killed already during their first mission against Krakoa. Telepathically sensing their deaths, Xavier grew 
severely depressed and Hank McCoy, the sole X-Man who hadn’t been with the team, came to care for him. He invited Moira MacTaggert to help, who brought her ward, Rahne Sinclair, with her. When Nefaria held the world hostage, Hank asked Xavier to assemble a new team but he refused. Hank used Cerebro to find and call in several new mutants, as well as Avengers Quicksilver and Scarlet Witch. They were transported to Colorado but so was Rahne, whom they didn’t realize was a latent mutant. The team fared badly against Nefaria, until Xavier finally got involved. Sensing that Rahne was a mutant, he telepathically activated her mutation and helped turn the tide. He later introduced himself to the team and asked they stay together, which they did (apart from the borrowed Avengers).
Ever wonder what had happened if not Cain Marko but Charles Xavier touched the Gem of Cyttorak? Well, there is one alternate reality, depicted in What if (2nd series) #13, where exactly 
that happened. While Cain remained human and escaped from the crumbling temple ruins, it was Charles who became the Juggernaut and had to dig himself out for years. By the time he got free, Magneto had already recruited most known mutants of the era and started terrorizing humanity, but Juggernaut Xavier quickly defeated him and took over his mutant empire. From there, it quickly turned into a mutant tyrant regime and some of the more idealistic mutants among Xavier’s ranks felt this was not right. These few were approached by Cain Marko, who, in the meantime, had allied up with Magneto, for one single goal – get rid of Xavier. Eventually they succeeded, ejecting Juggernaut Xavier into open space.
The importance of Charles Xavier can be best measured by looking at a reality where he died. Accidentally murdered by his time-traveling son, Legion, who had meant to kill Magneto instead, Xavier’s death caused Magneto to follow his friend’s dreams and create the X-Men instead. However, thanks to the events that led to Xavier’s death, the Darwinist mutant, Apocalypse, started a merciless war that turned the world into a living hell – the so called Age of Apocalypse.
In the timeline shown in What if (2nd series) #77, Legion went even further into the past and managed to kill Magneto. As a result, mutants were not feared at all in this reality, and the X-Men were media heroes. However, they had also never been really tested in battle. Xavier was worried about the state of the team and about strange mutant presences detected by Cerebro, but his superior, Forge, ignored his premonitions. Eventually, the X-Men were attacked and slaughtered by Apocalypse and his troops. Former X-Men, Cyclops and Phoenix, came to help. While Xavier died killing Apocalypse, Phoenix took out his troops, destroying most of Washington in the process. Jean and Scott took over the school, raising a new mutant generation in a now more hostile climate.
One Earth’s heroes weren’t as lucky after the Secret Wars, finding themselves stuck on the Beyonder’s Battleworld, as seen in What if (2nd series) #114. Continuing to fight the super-
villains who had been transported to the place too, eventually they ceased their wars after there had been casualties on both sides. The survivors spent the next decades on the planet, marrying each other and having children. While some of the X-Men had perished, Xavier was still alive, making use of Iron Man’s armor. He often told Storm and Wolverine’s daughter, Kendall, about how life on Earth had been for mutants, especially with anti-mutant hysteria on the rise.
The version of Charles Xavier from the Ultimate Universe was very similar to the regular one, though there were some minor differences. Xavier was married to Moira MacTaggert, a failing marriage that produced one son, David, who was later to become the mad Proteus. Xavier left Moira to work together with Magneto, but their goals became different ones and, when Xavier tried to flee, Magneto crippled him. Xavier founded the X-Men and was somewhat sneakier and 
more unscrupulous when it came to attaining his dream. Unlike most other known counterparts of the professor, this Charles Xavier also had minor telekinetic abilities.
Charles became the target of an assassination attempt when Cable, a time traveler, came from the future looking to kill him. Another time traveler, Bishop, came to help Xavier but arrived too late, as he was seemingly killed in an explosion. However, it was all a trick and “Cable” was actually an older version of Wolverine. Xavier had been teleported to the future, where he discovered the world had suffered a great catastrophe caused by a mutant named Apocalypse. Whilst Xavier trained with Cable in the future, Apocalypse was rising to power in the past and the X-Men were powerless to stop him. The time came for Xavier to travel back in time and he took on Apocalypse himself, only to be soundly beaten by the villain. Before he could be killed, Jean Grey turned into the Phoenix and saved him. She then destroyed the villain, seemingly killing herself in the process. Humbled by her sacrifice, Xavier vowed to use the X-Men to make a positive change in the world. Unfortunately for him, he wouldn’t live to see his dream come true, as Magneto unleashed his ultimate attack against the human population. After devastating New York with a tidal wave, Magneto personally sought out Xavier and snapped his neck, preventing the telepath from getting in the way of his plans.
In the Mutant X timeline, Xavier’s and Magneto’s roles were somewhat reversed. Following their original meeting in Israel, they continued to work together, at one point facing the Shadow King. His friend’s life at stake, Charles absorbed the evil telepath’s energy, and was a changed man ever since. Magneto noticed Xavier isolating himself, though there wasn’t much he could do about it. While Magneto focused on the dream and created the X-Men, Xavier vanished and was only heard from again years later. In the meantime, he had sought out nearly every known telepath and killed them to add their mental energies to his own. He was now fanatically proposing mutant superiority and it took the combined might of Magneto’s X-Men, Havok’s The Six and Apocalypse’s Horseman (all usually at odds with each other), to take him down.
After the reality-hopping Exiles were assembled, the first reality they were sent to in order to fix was some timeline where humanity had long declared Zero Tolerance on superhumans, and all mutants and other super-powered individuals were incarcerated, Charles Xavier being among them. [Exiles #1-2] The Exiles believed that their mission order, “Find the one who would lead you. Find your greatest teacher,” referred to the telepath, but after they busted him out of prison, they painfully learned that this counterpart of Xavier did not believe in peaceful coexistence. Instead, he set out to destroy humanity with the help of some other super-humans he helped to escape, including the Juggernaut. Eventually, though, he was killed by the Mimic, while some other members of the Exiles liberated Magneto, it being he to whom the cryptic message referred.
A time-traveling experiment gone wrong created another divergent timeline, one in which present day heroes already emerged in the 17th century, the year 1602 to be precise. Carlos Javier found 
a haven in tolerant Elizabethan England, where he had a small school for the sons of gentlefolk, actually a place to train the hated “witchbreed” – as mutants were referred to. With James succeeding Elizabeth as England’s monarch, Javier’s people were to be arrested, but Nicholas Fury joined them on a quest save the Fantastic Four, instead. Eventually, they ended up in the American colony of Roanoke, where Javier also took in the children of his old friend and foe, Enrique, the former Grand Inquisitor.