Dr. Bumby is helping Alice forget about her traumatic past. However, he has darker motives.
It is revealed near the end that he is responsible for ruining Alice's life by raping her sister, Lizzie, who had previously rejected his romantic gestures, and burning her and their parents alive inside their home. Bumby is confronted in the form of the Doll Maker on board the Infernal Train that is attempting to destroy Wonderland, a construct the real Bumby put into her mind to push her back into insanity so that even if she remembered the truth of the fire that claimed her family's lives, her accusations would be dismissed as the mad ravings of a lunatic. After Alice destroys the Doll Maker, she takes back control of her mind and kills Bumby in the real world by pushing him in front of a subway train, avenging her family and bringing him to justice.