In a Pokemon Red join Team Rocket fanfic, the main character could be a disillusioned trainer. Maybe they've lost a few too many battles and are looking for a new way to gain an edge. Team Rocket seems like an alluring option. They join up and are immediately thrust into the world of illegal Pokemon trading. However, they soon meet a friendly Pokemon that shows them kindness despite their new allegiance. This makes them question their decision to join Team Rocket and they start to think about how they can use their new position to actually help the Pokemon instead of harming them.
Maybe there's a rogue Pokemon trainer. This trainer is jealous of Dawn's skills and the attention she gets. When Dawn joins Team Rocket, this trainer sees it as a chance to expose her as a fraud. He or she then tries to stop Dawn and Team Rocket's activities, thinking that they are up to no good, which they are, but the trainer has his own self - centered motives.
One interesting storyline could be Team Rocket actually helping Ash in a dire situation. Maybe they realize that a greater evil is about to destroy the Pokemon world and they decide to team up with Ash for once. Their skills in stealing and sneaking around could be useful in gathering information about this new threat.
Well, the plot might start with a trainer who is a bit of a rebel. They don't like following the normal rules of the Pokemon world. Team Rocket notices this and recruits them. As part of Team Rocket, they participate in raids on Pokemon Centers to steal medicine for their own Pokemon. However, during one of these raids, they encounter a very sick Pokemon that needs that medicine desperately. This makes them question Team Rocket's motives. They then start to secretly work against Team Rocket from within, trying to protect the Pokemon and the integrity of the Pokemon world.
One idea could be that Ash feels betrayed by his friends because they always overshadow his achievements. So, in a fit of anger and disappointment, he decides to join Team Rocket. He might think that with their resources, he can finally become a more powerful trainer on his own terms.
Well, in such a fanfiction, the plot might involve Team Rocket devising a clever plan to capture Dawn. Maybe they use some new and devious Pokémon or traps. They could be after her Pokémon for some evil scheme, like using them to take over a Pokémon Contest Hall.
Well, perhaps she is a captive of Team Rocket in the fanfiction. They might be using her for some sort of experiment related to Pokemon, like trying to extract some special power from her that they think is linked to her bond with certain Pokemon. And Lillie has to find a way to escape while also protecting the Pokemon around her.
Some of his more loyal Pokemon might try to resist the change. For example, Pikachu could use electric shocks to try and jolt Ash back to his senses. Pikachu has a strong bond with Ash and would be very confused and sad about his decision to join Team Rocket.
One possible plot could be that Dawn, for some reason, gets disillusioned with her regular Pokemon journey. Maybe she has a series of losses that make her question her methods. Team Rocket, seeing an opportunity, convinces her that they have a better way to train and use Pokemon. She then joins them, initially helping with their small-time schemes, but gradually realizes that their actions are unethical and has to find a way to break free.
Ash is obviously one of the most popular characters. He's the main character of the Pokemon anime, and in fanfictions, his adventures with or against Team Rocket are always interesting. People like to see how he reacts to different situations that Team Rocket creates or how he manages to outwit them.