BIOGRAPHY - Page 6
Xavier wasn’t aware that there had been ramifications to his deed, which would lead to the darkening of his 
own mind. Indeed, the frustrations in his life were mounting. There was the threat of hate groups, like the Friends of Humanity, whose leader, Graydon Creed, was running for the presidency. Also, sure that their duties and priorities would always come between them, Xavier broke off his long-distance relationship with Lilandra. Finally, a mutant named Dennis Hogan, looking for asylum, more or less died on the X-Men’s doorstep and Xavier shared the pain of his death. [X-Men Unlimited (1st series) #5, X-Men Prime]
All these elements of frustration, as well as the darkness he had unwittingly absorbed from Magneto, affected Xavier, causing him to grow colder at times and even act unscrupulously. 
This, combined with all of the rage he normally suppressed ultimately led to the emergence of a second personality – Onslaught. Before he would reveal his true identity, Onslaught vexed the X-Men and their allies, such as Cable or Xavier's hated stepbrother, the Juggernaut. At the same time, Onslaught was gathering allies and observing Nate Grey and Franklin Richards, two mutant boys essential for his plan. Finally, he took over the Professor - his goal being to achieve Xavier’s dream of coexistence through Magneto’s means: have mutants rule the world. To that end, Onslaught had reprogrammed the Sentinels to terrorize the baseline human population of New York City, while he kidnapped Nate and Franklin, intent on using their immense powers for himself.
The heroes eventually managed to free a powerless Xavier from Onslaught, but found that Onslaught, who still held Franklin and Nate prisoner, had evolved and now could exist independently from Xavier. However, when Onslaught learned from Nate Grey’s mind that the mutants who ruled his native reality, the Age of Apocalypse, were no better than the humans in the main universe, possibly even worse, Onslaught decided that neither species was worthy to survive and as such intended to destroy all life. It was only through the sacrifice of the non-mutant heroes that Onslaught was destroyed. Xavier, however, while managing to save Nate and Franklin with the help of the mutat known as Joseph (believed to be a de-aged Magneto at the time) was left with his telepathic abilities gone. [Onslaught crossover]
In the aftermath of Onslaught, Xavier not only had to deal with the guilt for his role in the tragedy but also with the possibility of facing criminal charges. While the X-Men believed him to be in the sympathetic hands of Val Cooper, Xavier 
was confined by the mutant-hating Bastion, the leader of Operation: Zero Tolerance. Xavier wasn’t helpless, though, which he proved when he helped the newly created lifeform, Nina, a girl with vast psychic powers, to escape from Bastion’s clutches. [Uncanny X-Men (1st series) #337, X-Men (2nd series) #57, Onslaught: Epilogue] Staying behind as a prisoner, Xavier had to endure Bastion’s constant attempts to humiliate him, all the while he set events in motion that turned the X-Men into fugitives. [Operation Zero Tolerance crossover]
Once Operation: Zero Tolerance was shut down, Xavier was busted out of prison by a new Brotherhood of Mutants, led by the Toad. Bastion’s actions had inadvertently created a sentient 
Cerebro, which was now kidnapping mutants in an attempt to catalogue them. Being on the run from this Cerebro, the Brotherhood needed Xavier’s help. Although without his telepathy, Xavier was still able to teach them the value of teamwork, which helped the group to survive and evade Cerebro’s agents for some time. Looking for Xavier, the X-Men tracked the Brotherhood to their hiding place on Alcatraz, only to witness them in another conflict with Cerebro. Eventually, though, the construct was defeated, partially because the Mannite girl, Nina, reactivated his telepathic powers, allowing the professor to link with Cerebro and make it see its error. [Hunt for Xavier crossover]
Reunited with his X-Men, Xavier sensed a threat and began to recall his helping the two Destine women to banish Synraith years ago. Synraith now struck again, seemingly trapping Xavier, Colossus, Gracie and Cuckoo in a limbo, while setting up the other members of the X-Men and the Clan Destine against each other. Only later, it turned out that Synraith had actually set the Danger Room against the Clan Destine and the few X-Men that were there and that the banished members were simply in another section of it. Together, the two teams managed to banish Synraith once and for all. [X-Men & Clan Destine #1-2]
With recent events, Xavier briefly questioned his dream again. It was shortly thereafter that the X-Men had another conflict with Magneto, who seemed again bent on trying to destroy humanity. The battle ended unexpectedly with the UN conceding Genosha as a new mutant homeland to Magneto and Wolverine being furious with Xavier for keeping him from taking revenge and killing Magneto. [Magneto War crossover] During the X-Men’s next adventure, the two men had to overcome their differences. Trapped in a dimension with different laws of physics, their mutant powers acted in bizarre, unprecedented ways. When Xavier’s astral form made contact with Logan’s body, he was pulled inside. Charles and Logan had to coordinate their moves from then on and the experience actually helped them to understand each other’s point of view better. [Uncanny X-Men (1st series) #368-369, X-Men (2nd series) #88]
When the X-Men returned to Earth from a mission on the Skrull homeworld, Xavier had the feeling that someone had breached his mind. Suspicious, he outwardly grew stricter toward the 
X-Men and apparently more erratic, to the point where he fired almost all the X-Men. Actually, though, he was merely trying to ferret out the traitor he sensed among their midst. Not fully sure who of the team had been replaced by an imposter, Xavier first disbanded the group to make sure that, whatever their plan was, it wouldn’t work. Charles didn’t expect some of his students to carry on, as Cyclops and Phoenix gathered a small X-Men squad. This new team hit off on a bad start when Wolverine was killed by Apocalypse’s Horseman, Death. Investigating the body, Xavier discovered that it wasn’t really Logan, but the traitor he had been looking for: a Skrull who had been mimicking Wolverine, the real deal having been captured by Apocalypse and transformed into Death. [X-Men (2nd series) #90, Uncanny X-Men (1st series) #371, 375]
This was merely a prelude to a climactic battle with Apocalypse, who wanted to lure together the fabled “Twelve,” a dozen special mutants, Xavier included, whose energies in combination would give Apocalypse omnipotence. In the aftermath of the fight, Cyclops sacrificed himself and merged with Apocalypse. During the conflict, the X-Men had also learned of a group of Skrull mutant youngsters, who had been branded outcasts from their species and were exploited by both the Skrull military and Apocalypse. Xavier knew that they needed some of his training, so he decided to leave Earth together with Cadre K, as the Skrulls called themselves. [X-Men (2nd series) #90, Uncanny X-Men (1st series) #379]