One idea could be a crossover with a popular RPG. The protagonist of Cave Story could find themselves in the world of the RPG, facing new enemies and having to learn different magic or combat systems. For example, if it's a Final Fantasy - like world, they might have to deal with complex job classes.
A crossover with a sci - fi game. Maybe the Cave Story world gets invaded by aliens from a space - faring game. The main character then has to use his skills and the unique weapons from Cave Story, like the Polar Star, to fight off these extraterrestrial threats. He could also team up with some of the sci - fi game's characters, who might introduce him to advanced technology like energy shields or teleportation devices.
One idea could be exploring the backstory of the Mimiga. Maybe there was a time before the events of the game when they had a more complex society. Another is to focus on Quote's life after the main story, like how he adapts to a more peaceful world. Or you could create a fanfic where an unknown Mimiga has special powers and becomes a key figure in saving the island from a new threat.
Another option is a crossover with the Pokémon world. The Phantom Thieves could travel to a region in the Pokémon world and discover that someone is using Persona powers to make Pokémon act out of control. They would need to catch Pokémon themselves and use their combined powers of Personas and Pokémon to stop the bad guy. It would be interesting to see how they interact with Pokémon trainers and the whole Pokémon ecosystem.
A cool plot could involve the Persona 5 crew going back in time to the events of Persona 3. They might end up interfering with some of the original events, which could have unforeseen consequences. For example, they could accidentally change the way a key character in Persona 3 awakens their Persona, and then have to figure out how to fix it while also dealing with the Shadows in that era.
One idea could be to cross it with another popular RPG. For example, having the Persona 4 characters enter the world of Final Fantasy. They could interact with the different races and magic systems there. Another could be a crossover with a detective - themed anime. The Investigation Team could team up with the detectives from that anime to solve a mystery that spans both worlds.
Another plot could involve a crossover with the Punisher and the X - Men. Frank Castle might find himself in a situation where he has to work with mutants. He could initially be distrustful but then realize they are fighting for a similar cause against a common enemy that is targeting both humans and mutants. For example, a group of anti - mutant and anti - vigilante fanatics.
One idea could be a crossover with Peter Pan. Tinkerbell could meet characters from another world, like Alice from Wonderland. She might be confused by the strange rules and creatures there, and her magic could interact in unexpected ways with the Wonderland magic.
Another plot could involve a crossover with a post - apocalyptic world. The Boys find themselves in a world where society has collapsed, and they have to team up with the survivors against new threats. This could bring out new sides of the characters as they are forced to adapt to a completely different environment and face challenges they've never faced before.
One idea could be to cross over the characters from 'Percy Jackson and the Olympians' with those from 'The Kane Chronicles'. For example, the demigods and the magicians could team up to fight a common enemy that threatens both the Greek and Egyptian mythological worlds. Maybe a new dark force that has the power to disrupt the balance between the two realms.
One idea could be a crossover with Minecraft. The Terraria characters could find themselves in a Minecraft world filled with blocky landscapes and different mobs. They would have to adapt to the new building mechanics and find ways to combine their own abilities with the resources available in Minecraft.
One idea could be to cross it with a post - apocalyptic zombie world. The characters from Into the Badlands have to fight both zombies and their usual foes. They could use their martial arts skills in new ways, like using katana to slice through hordes of zombies.