The darkness is within the souls of the boys themselves. Simon understands this all too well, which is why he recognizes that the so-called beast is purely mythical and exists solely in the minds of the boys themselves. For much of the modern age, the term "darkness" was often used to describe certain aspects of remote, exotic cultures in distant corners of the globe. Such cultures were so alien to Western man, so totally "other" that they were regarded as backward and primitive.
The boys in Lord of the Flies pride themselves on being from wealthy, privileged backgrounds, representatives of the British Empire and its great civilizing mission. But as the action progresses, they too succumb to the "darkness" that colonialist discourse regards as the sole preserve of the so-called lesser races. This indicates that darkness and all it represents is within the soul of each individual, irrespective of their background, no matter how ostensibly "civilized" they may be.