There is no definitive answer to this question, but a number of possibilities. It is all the more important to consider this question in light of the fact that the outcome of the film of The Natural is very different from and much more optimistic than the novel. The easiest answer is that, at his last at-bat, Roy does not have Wonderboy. More important, perhaps, the last pitch Roy gets is a "bad ball," but he swings at it anyway. Throughout the novel, it is implied that Roy's tendency to swing at bad balls is because Wonderboy always helped him hit those balls; in this sense, Wonderboy is not only a weapon of power, but also a sort of crutch, hiding a weakness. Pop has already expressed reservations about Roy's tendency to swing at bad balls; without the supernatural aid of Wonderboy, Pop's warning comes true.
There is an alternate answer to the question, however. Roy may be destined or fated to strike out, much as he strikes out the Whammer fifteen years earlier. The idea of the vegetative myth, around which much of the legend of the Fisher King—and therefore The Natural—is based, a cycle repeats itself every year, as the flowers, insects, and other beings die in the fall, to be replaced by new life the next year. In being struck out, Roy may simply have been fulfilling the cycle he started when he struck out the Whammer so many years earlier.