Charles Xavier's fate in the comics is not straightforward. Sometimes he's alive, sometimes he's dead. It all depends on the writer's creative decisions and the direction of the story at that time.
Well, in the current state of the comics I've followed, Charles Xavier remains deceased. However, comics have a way of bringing characters back or introducing alternate timelines and universes, so there's always a possibility for his return in some form.
There might be an older mutant who has already given up on using their powers and lives in seclusion. Charles Xavier meets this mutant while hiding his own powers. They start to share their experiences and the older mutant gives Xavier some unique perspectives on power, identity, and hiding. This relationship could be a central part of the fanfic, with both mutants learning from each other and evolving as characters.
One possible scenario could be that in the fanfiction, Eric and Charles are in the middle of a heated ideological battle. Eric's powers get out of control, accidentally injuring Charles. This could lead to a moment of self - reflection for Eric, realizing the consequences of his actions. Meanwhile, Charles' friends and allies would be in a rush to save him, with his students at the Xavier School worried sick about their mentor.
A fanfiction might start with Charles being seriously injured in an unexpected attack. Erik, who has always had a strong connection with Charles, is enraged at first. But then he realizes that he needs to be calm to help Charles. He takes Charles to a safe place and tries to find a way to heal him. Along the way, they face many challenges, both external threats and internal emotional struggles. As time passes, their bond becomes even stronger through this difficult experience.
In the official X - Men universe, Charles Xavier is a heroic and ethical character. Fanfiction can sometimes deviate wildly from the original canon. Just because there is such fanfiction doesn't mean it has any basis in the real lore of the X - Men. Most likely, it's a dark and untrue creation of some fans who like to explore extreme or controversial ideas in their fictional writing.