The full story
X-Men: Apocalypse opens with a god waking. Apocalypse has slept for centuries, and he wakes to a world he considers weak. He sees mutants hiding from humanity. He sees humans asserting dominance over mutants. He sees chaos. His response is to restructure everything according to what he believes is natural law: the strong rule, the weak serve.
Apocalypse is not presented as illogical. He is presented as someone whose logic is predicated on a false premise. He believes that power is moral justification, that strength grants the right to rule. If you accept that premise, his conclusions follow logically. The film shows us people who do accept that premise—Magneto, initially, accepts that mutants are superior and deserve to dominate. Apocalypse offers Magneto a vision where this dominance is guaranteed.
But the film also shows us what this dominance actually means. It means thousands of deaths. It means destruction. It means reshaping the world against the will of every person living in it. Apocalypse is willing to cause infinite suffering to create what he considers a perfect order.
Magneto must confront the difference between believing mutants should be powerful and believing they should rule through force. His personal loss—the destruction of his family—forces him to recognize that his alignment with Apocalypse has consequences. He agreed with the principle of mutant superiority but did not fully confront what that meant when actualized.
Professor Xavier represents the counter-vision: that power should be restrained, that difference should be respected, that coexistence is possible without dominance. Xavier can barely move. He is physically weak compared to Apocalypse. Yet his vision of the world is stronger than Apocalypse's vision, not because it is more powerful, but because it respects the autonomy and dignity of those he would lead.
The final confrontation is not between Apocalypse and his most powerful ally. It is between Apocalypse and the people he tried to control. They choose to resist, not because they are stronger, but because they have decided that autonomy matters more than safety. Apocalypse cannot understand this. To him, the choice to resist when resistance is futile is incomprehensible. But to the X-Men, it is the only choice that matters.