How does a Gengar come to exist?
The answer is much simpler than one would think. There are multiple instancess from which Gengars are born. Either way, they are more or less an animated shadow of their happy counterpart. A doppelgänger, to be exact. This German word can be defined as "a paranormal double of a living person, typically representing evil or misfortune".
Each instance is similar in that a Clefable loses its innocence, and their "shadow" takes a life of its own. When a Gengar is born, the Clefable's memory of the horrible event is erased. This leaves many opportunities for a Clefable to essentially "create" a Gengar, should they experience multiple tragedies in their lifeitme. In a way, Gengars are a way to preserve Clefable's innocence. This is the main reason that no one has ever come across an evil Clefable.
The Tragic Death of a Trainer
Clefables are a loving Pokémon, making them popular companions for trainers all over the world. With so many of these trainers wandering (many of them by themselves, say for their Pokémon), tragedy is bound to strike. Some become lost in the wilderness while travelling in a foreign region, or have life-threatening accidents. One way or another they die. Their Pokémon are left alone to fend for themselves. Clefable's innocent mind can't handle such a loss. Gengar is born, and the Clefable forgets that it ever met the trainer.
A wild Clefable obviously doesn't have this kind of bond. There are many other, perhaps less extreme situations that can spawn a Gengar, usually involving some kind of highly negative incident. For example, if survival becomes too difficult, a Clefable may slowly start to turn bad and act maliciously towards others of its kind to raise its odds. This can include stealing food, shelter, or any other kind of thievery. Each time, it begins to feel a sense of enjoyment from committing these acts. Once it reaches a certain level (such as murdering another Clefable), the shadow takes life and Clefable returns to its normal harmless self.
One thing is for sure: if you have ever caught a Gengar, something terrible has happened to the Clefable that it came from. Perhaps it would be a good idea to keep that in mind the next time you decide to go after one.