Another thing that could occur is that Ash's friends would be very suspicious. They might think Ash has gone to the dark side. So they could try to rescue him. This would lead to a lot of drama and action. There could be epic battles between Ash's friends and Team Flare while Ash is caught in the middle, trying to figure out what to do and where his loyalties truly lie.
His Pokémon might be confused at first. They are used to Ash being on the side of good. But if Ash believes he can change Team Flare for the better, his Pokémon might go along with it. However, they could also sense the danger and be on high alert. For instance, Pikachu's electric attacks might be more charged up than usual, ready to protect Ash at any moment.
One idea could be that Serena is initially deceived by Team Flare's false promises of a better world for Pokemon. She might see their flashy technology and think they can help her become a stronger trainer. But as she gets deeper into the team, she starts to realize their true, evil intentions, like stealing Pokemon for their own gain.
Ash could use his Pokémon. Pikachu, for example, could use its electric attacks to short - circuit any devices or barriers holding Ash captive. His other Pokémon like Charizard could also help by using their strength or special abilities to break free.
Another possibility is that Serena discovers a secret within Team Flare that could change the whole dynamic of the Pokemon world. It could be a powerful weapon or a hidden plan that is far more dangerous than anyone thought. She then has to decide whether to use this information to her advantage within the team or to try and get it out to the people who can stop Team Flare. This would put her in a very difficult position as she's already in deep with the team.
In a fanfiction where Ash joins Team Rocket, it could lead to some really interesting storylines. Ash has a lot of knowledge about Pokémon training that Team Rocket lacks. He could potentially teach them new techniques, but at the same time, his moral compass would be constantly at odds with their devious ways. Maybe he joins them because he's somehow tricked or he has his own secret plan to take them down from the inside. It would be a great opportunity to explore different aspects of his character and how he adapts to this new situation.
One possibility is that Ash joins Team Galactic under some sort of misunderstanding. Maybe he thinks they are a group with good intentions at first. Once he realizes their true nature, he has to figure out a way to escape or stop them. This could create a lot of tension and action - packed scenes in the fanfiction.
Well, he could be used as a bargaining chip. Team Flare might try to exchange Ash for some powerful Pokémon or valuable items. They could also try to force Ash to reveal any secrets he has about powerful Pokémon or rare items he's come across during his travels.
Another plot twist could be that Team Flare's leader has a change of heart after kidnapping Ash. He realizes that Ash's pure love for Pokemon is something that could be used for good. So, instead of harming Ash, he decides to team up with Ash to fight against a common enemy that threatens both their interests and the Pokemon world as a whole.