There is no canon source so saccharine that it can't produce good fanfic about villains, if people are motivated enough. It may surprise people that Pokemon, unabashedly a kids' craze, has any good fanfic, let alone any good fanfic about villains. But there are certain significant themes that are underplayed in the show itself, but which clever fanfic writers can pick up on. Like the dilemma of being a sentient being with powers, whose species is defined as animals to be captured and enslaved. Like the potential problems lurking behind the scenes in a world that produces hosts of identical women to staff police forces and veterinary hospitals. Like the dark side of a sport that involves enslaving near-sentient beings and teaching them to fight each other.
Oh, yes, there is potential for explorations of the dark side in Pokemon as well. And I'll prove it. Read on...
April 2000 Feature Fanfic: Mewtwo, Escaped by Tiffany
This is not so much about the canon Mewtwo as about the second of a series of engineered Mewtwos, this one female... a powerful fighter who fears humanity as much as they fear her, but who has to learn to rely on them if she wants to be free.
Team Rocket:
Meowth
Somehow I feel that there's a tragedy in Meowth that hardly anyone ever deals with. Here's an intelligent being who can talk, clever and ambitious, whose entire life is geared around pleasing a single human who has rejected him... who loves money and is probably legally not allowed to use it... who is disconnected from his own species by the gift that enables him to speak like a human, yet not granted the rights of a human either. A few people seem to have seen some of the potential in Meowth that I have.
One take on Meowth's origin. How a desperate street kitten with no mother and no future managed to learn to talk like a human, gain the grace of the powerful Giovanni, and lose it again.
An Alakazam forms an anti-human movement of Pokemon, and Meowth joins as its spokesPokemon, dreaming of a world where he can be valued as an intelligent being... but what price might he have to pay?
Jessie and James
These two are usually portrayed as doofuses, for the simple reason that, as shown in the show, they are doofuses. But you have to wonder what drives people to keep trying, time and time again, in the face of repeated failure?
The Letter R by Nethilia.
A dark version of Jessie's origin.
The Pikachu Project by Sailor Mac.
A parody of the Blair Witch Project.
Giovanni
Giovanni is enough of a mystery man that any number of motivations can be ascribed to him. Is he evil? Is he totally ruthless? Or does he have a soft spot in his heart for some people?
My Mother: by Leto.
Giovanni remembers his mother, the woman who made him who he is today.
Miscellaneous
I include new members of Team Rocket, other members, and other such here.
A Persian's Tale: by Shadowcat.
The origin of Giovanni's enigmatic favored pet.
Villainous Pokemon:
Mewtwo
The character pretty much responsible for my reading Pokemon fanfic, Mewtwo is one of the most complex characters in the Pokemon universe. A super-Pokemon created by genetic engineering, Mewtwo is tormented by the feeling that he is not a real being, and at the same time convinced of his own superiority to humanity and other Pokemon, and this conflict drives him to do any number of bizarre things, like try to destroy the world to punish those who created him. Very mature, Mewtwo. :-)
(Nothing here yet except the Feature, but more coming soon!)