The Boy Who Disappeared, also called Boy X, was a boy that Sophie saw right before she hit her head on the sidewalk and manifested as a Telepath. He wore a bramble jersey. Sophie couldn't see his face clearly, because he was wearing an addler - a gadget prevented people from focusing on the wearer. The boy appeared out of nowhere and saw Sophie staring at him, then disappeared. Sophie started to run after him, but she tripped and hit her head on the sidewalk, causing a trip to the Emergency Room. It was during this trip that Mr. Forkle triggered Sophie's Telepathy. Mr. Forkle removed her memory of this incident, and Sophie only got the memory back in Book 4: Neverseen.
Sophie had written in the corner of her "sparkly pink journal", the Boy Who Disappeared. Keefe helped her recover what she'd written when she realized that the pages were missing using the pencil technique.
Sophie and her friends searched everywhere for the Boy Who Disappeared. They thought that he had attended Exillium, and searched through the records that Dex had broken in to. They thought that Boy X was the Psionipath that Sophie and Biana had encountered in the woods, Ruy Ignis.
However, towards the end of Book 4, when Sophie and her friends had just escaped from the ogre city, Ravagog, they are captured by Fintan and Brant. The pyrokinetics tell Alvar that the game is over. Alvar, who went with them on the mission to be their guide, joins Brant and Fintan and is revealed to have been with the Neverseen all along. Alvar was the Boy Who Disappeared and he was searching for Sophie. Sophie and her friends leap away just in time, telling everyone back home the news.