As players watched Red seemingly stumble around during the playthrough of Gen 1, art began to be produced that depicted Red under the influences of voices in his head that mirrored the game commands inputed via the streams IRC chatroom. Red's extremely erratic movements were commonly contrasted sharply against the many non-moving NPCs within the game including a large percent of trainers and the gym leaders/Elite 4. The suggestion came that these NPCs would see Red moving in a largely random way, unable to guess what he would do next and came to the conclusion that he must either be mentally challenged or under the influence of something much more sinister, thus The Voices became an integral part of the TPP Lore.
Originally, much of the community viewed these voices to be a result of Red suffering from schizophrenia or another psychological disorder. Over time however, depictions began to represent the origin of the voices as otherworldly, or from a higher presence. Some interpretations even have the voices coming from the old gods, of which the Dome, Lord Helix, and Old Amber are believed to be. After his defeat of Blue, Red was believed to have been freed of the voices.
At the beginning of Gen 2, AJ is believed to be afflicted by the voices as well in many stories. Some versions have the voices being a group of unseeable Unowns, a group of Pokemon introduced in original Pokemon canon in generation 2. Many interpretations view AJ as actively fighting the influence of the voices, and perhaps rebelling against them by challenging Lord Helix atop Mt. Silver. AJ was also believed to be released from the influence of the voices after his defeat of Red at the end of Gen 2.
After this there is some debate as to what happens to the voices. Some even believe that they were temporarily locked out of the Pokemon universe, others believed that they simply waited for the right moment. Eventually, they came to the trainer A. Unlike Red or AJ, whom were chosen by the voices, A summoned them to her, possibly bringing them back to the Pokemon Universe.
Increasingly in later generations, the voices have been interpreted as Unowns.