Glitch in the matrix

[T'Chenka]

Other than the photographs disappearing, it sounds like an undercover extra-terrestrial family up and left and "neuralyzed" the town (Men In Black memory erasing) on their way out. "Scott" was a young male extra-terrestrial with adult parents working undercover. Somehow the author was not neuralyzed. Doesn't explain the photos missing though.

Plot twist, Scott (OP and Atlas poster) is recounting what happened when he was a child living with his parents undercover on Earth with a young human boy who loved him.