The idea was that when the Dark Phoenix is taking over, Jean's skin darkens, veining appears on her face, and her eyes go black.

Dark Phoenix is the secondary antagonist of X-Men: The Last Stand - this time caused by Jean apparently going insane. In the film, Professor Xavier recognizably remembered this alternate personality of Jean Grey by its other name "The Phoenix", whom he sees as in his own words, "a creature all desire, joy, and rage".