He/she is of unknown origins, but Goddramon was present at the birth of the universe. However, due to the Problem of Evil, no such being could possibly exist, let alone stabilise, so his/her personality and form ended up split into two beings: Harmony and Chaos, the power of Goddramon split between them. Harmony's abilities revolve around creation, whilst Chaos' revolve around destruction, neither being both Omnibenevolent and Omnipotent. The pair ended up hating each other, however, and their conflict and constant competition for supremacy lead to the formation of the structure of the universe.
Goddramon is the DNA digivolution of two Biomerged digimon, Gallantmon and Sakuyamon. It's power and the fact it is comprised of the minds of Takato, Rika, Guilmon, and Renamon (not to mention the mortal enemies Chaos and Harmony) means it can not remain in that form without causing untold damage to the universe. It appeared in Book Four to defeat Yggsdrasil before separating once again.