Actually Mystique had duped Shepard, and had communicated a plan to Fantomex on a sub-aural level that he could hear but others could not - by morphing her vocal cords. She and Fantomex grabbed Shepard and Fantomex revealed that Shepard was in fact Prudence's brother, who had joined hIS sister, who now inhabited the body of Steinbeck and had taken on the "Quiet Man" identity. Mystique chopped off Shepard's hand to get at his teleporter watch and went to deal with The Quiet Man.