Like many things in the Persona universe, Philemon traces his creation back to the work of Swiss psychiatrist Carl Jung (1875-1961). Specifically the work Liber Novus or as its more often called the Red Book after its red leather binding. The Red Book is a manuscript Jung worked on throughout his life, the 205 pages contain images he drew along with text written with calligraphic lettering. Jung's heirs have guarded access to the Red Book, with researchers only allowed to study it beginning in 2001 and a published edition only appearing in 2009.
The Red Book was written by Jung under what he termed active imagination. Active imagination is a meditation technique where the subject allows his unconscious ideas to be translated into images, narrative, or personifications. It is during this active imagination that Jung in the Red Book says he encountered two spirit guides. At first he describes them as an old man and a young woman. He then names these two guides Elijah and Salome. With these two guides comes a black snake. The guides over time get transformed further. Salome becomes the anima, the unconscious male's feminine inner personality. Elijah becomes the spirit Philemon who Jung believed to regard superior insight and he communicated through the use of mythic imagery. These guides are what caused Jung to believe that there is more a person's psyche then what they themselves contain and so was the beginning of his theory of the collective unconscious.
After the kids play the Persona game and summon a demon, they are each transported to a dream world where Philemon meets them and grants them the power to summon "their many selves within" -- or Personae.
Persona 2: Innocent Sin
After the fight between Tatsuya, Lisa, and Eikichi they become unconscious, while knocked out the 3 meet with Philemon and are granted the power to use their personae.
Persona 3 and Persona 3 FES
Philemon may have appeared in Persona 3 in his butterfly guise. Only the playable characters who met Philemon could summon multiple Personae, but others, who had not encountered him, could only summon a single Persona. In Persona 3, this is explained to be due to one possessing the Wild Card. The only two characters to possess this ability in Persona 3 and its epilogue both had an encounter with a glowing blue butterfly, which may be Philemon. The name "PHIL" which welcomes the main character to the online game "Innocent Sin", may also be a reference to Philemon.
The save points throughout the game are blue butterflies flying in small circles. This is a sign that Philemon is still watching over the player.