X-Men: Evolution follows the story of Professor Charles Francis Xavier, who has the mutant ability to read minds. He searches for new mutants to train them how to use their powers for good and to prevent them from harming themselves and others at his School for Gifted Youngsters.
His opposition, Magneto "Master of Magnetism", is also searching for mutants, but for evil purposes. He has made Mystique, a shape-shifter, a principle of his high school to gather evil mutants and prepare them for war against non-mutants.
The most interesting aspect of the story is that all the heroes and villains attend the same high school. The classic battle of good vs. evil has begun again.