Perhaps a vengeful spirit that has a connection to a long - forgotten Pokemon legend. The spirit blames humans, including Wes and Rui, for the downfall of its kind in the past. So it uses its powers to cause chaos in the Pokemon world and tries to prevent Wes and Rui from saving the day.
A powerful and corrupt Pokemon trainer who wants to use rare Pokemon for his own evil plans could be a great antagonist. He might try to steal Pokemon from Wes and Rui or stop them from achieving their goals.
The main characters are Wes and Rui, of course. Wes is often depicted as a strong and determined trainer. Rui is usually portrayed as having a special bond with Pokemon and being very intuitive when it comes to understanding them.
One possible fanfiction could be about Wes and Rui's adventure in the Pokemon Colosseum world. They might face a powerful new trainer and have to use their unique Pokemon teams to win. Maybe they discover a rare Pokemon during their travels and have to decide what to do with it.
One idea could be that Wes and Rui embark on a journey to find a rare and powerful Pokemon that has the ability to heal the sick Pokemon in a particular region. They face many challenges along the way, like battling against a group of poachers who also want the Pokemon for their own greedy reasons.
An organization of rogue scientists who want to experiment on Pokemon could be the main antagonist. They might be trying to create super - powerful mutant Pokemon or find a way to control all Pokemon. If you're reborn as a Pokemon, they might capture you for their experiments. This could lead to a story where you have to escape from their labs and expose their evil plans to the rest of the Pokemon world.
Well, 'Wes and Rui: Unraveling the Mystery' could be a great fanfiction. It could start with a strange occurrence in the Pokemon world that only Wes and Rui seem to notice. As they dig deeper, they uncover secrets about the origin of certain Pokemon or an ancient power. Their relationship could develop as they face these mysteries together, and they might have to make tough decisions that affect not only themselves but also the entire Pokemon world.
A new, mysterious organization that is interested in controlling the legendary Pokémon. They see Latias as a key to their plan and Ash as an obstacle to be removed.
Perhaps an evil Pokémon organization. They could be conducting unethical experiments on Pokémon, and when they hear about the reborn Pokémon, they want to capture it for their research. They might believe that the reborn Pokémon holds the key to some sort of ultimate power or knowledge that they can use to take over the Pokémon world.
A powerful and greedy trainer who wants to capture Manaphy for its rare abilities could be the main antagonist. He might have a whole team of strong Pokemon and use underhanded tactics to try and get Manaphy.
It could be Team Rocket. Since they always cause trouble for Ash in the original series, in this fanfic, they might see Ash's transformation into a Pokémon as an opportunity to capture him and use him for their evil plans.
Team Rocket could always be the main antagonists. They might have a new and more devious plan to steal Ash's Pikachu and other rare Pokemon that Ash and Brock encounter on their journey.