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.
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.
Pikachu would probably be very confused at first. It's used to fighting against Team Rocket, not being on their side. It might resist and try to zap Ash to snap him out of it.
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.
Well, if Serena joins Team Rocket in a fanfiction, she might bring a new dynamic. Maybe she's forced to join at first. She could use her skills in battles and her knowledge of Pokemon to help Team Rocket in their schemes, but secretly she could be planning to take them down from the inside.
She might start off as a scared and naive character. But as she gets more involved with Team Rocket, she could become more brave and resourceful. For instance, she could learn how to fight back against Team Rocket's bullies using her wits and the help of her Pokemon friends.
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.