One idea could be that Sora and his friends end up in Equestria. They could team up with the ponies to fight a new threat that is affecting both their worlds. Maybe the Heartless are somehow being drawn to Equestria's magic and they need to find a way to stop it together.
Another concept could be that a pony discovers a keyblade. This pony then has to learn how to use it and embarks on a journey similar to Sora's. They might travel to different Disney - inspired worlds from Kingdom Hearts, all while still being connected to Equestria in some way.
One interesting plot could be that the ponies from MLP accidentally find themselves in the Kingdom Hearts universe. They might mistake the Heartless for some kind of dark magic creatures from their own world and try to fight them using their magic. For example, Twilight Sparkle could use her powerful spells to combat the Heartless while trying to figure out how to get back to Equestria.
Well, a great plot could be Roxas finding himself in a crossover with a Final Fantasy world. He meets some of the iconic Final Fantasy characters like Cloud or Tifa. They initially suspect him because of his connection to the Heartless and Nobodies. But as they get to know him, they realize he's on their side in the fight against a new enemy that is trying to use the power of both the Kingdom Hearts and Final Fantasy universes. It could be a story full of action, character development, and exploring the differences and similarities between the two universes.
One idea could be Aqua crossing over into a different Disney world, like Wonderland. She could have to navigate the strange rules and characters while still maintaining her Keyblade skills. Another could be a crossover with a Square Enix game universe other than Kingdom Hearts. For example, she might end up in the world of Final Fantasy and team up with some of those characters to face a new threat that somehow links both universes.
Well, perhaps in this fanfiction, the Organization XIII has a plan to use Elsa's powers for their own evil purposes. They manipulate events in Arendelle to make Elsa feel isolated and out of control. Sora, Donald, and Goofy show up and befriend Elsa, showing her that she can trust others. They then have to battle the Organization XIII members while also dealing with the internal struggles of Arendelle's characters, like Anna's determination to save her sister no matter what.
A possible plot is that the Soul Reapers discover the existence of Kingdom Hearts. They might think it's some sort of powerful spiritual object. Rukia could be the first to encounter a Keyblade wielder like Sora. Sora, in turn, could be intrigued by the Soul Reapers' powers and their way of dealing with the afterlife. The two groups could then join forces to stop a common enemy that threatens both their worlds. Maybe an ancient evil that wants to use the power of Kingdom Hearts and the souls in the Bleach universe for its own dark purposes.
Maybe Sora, Donald, and Goofy end up in the Naruto universe. They would be really confused at first. Sora could try to understand the concept of chakra and how it's different from the magic he knows. They could team up with Naruto's team to take on Akatsuki members who have somehow been influenced by the darkness in the Kingdom Hearts world.
Perhaps Voldemort discovers the power of the Heartless and tries to use them to his advantage. The protagonists from Kingdom Hearts then have to work with the Order of the Phoenix to stop Voldemort and the Heartless. The Hogwarts students could be fascinated by the Keyblades and the different worlds the Keyblade wielders have been to, and there could be a lot of cultural exchange between the two groups.
Another interesting concept is an OC who is a member of an organization that opposes Organization XIII in a different way. Maybe they use magic that is not based on darkness or light, but something in between, which causes them to be shunned by both sides at first.
One idea could be exploring the backstories of the new characters introduced in Kingdom Hearts 3 in more depth. For example, you could write about how they came to be in the different worlds and what their true motives are.
One idea could be a fanfiction where the characters from Kingdom Hearts watch their own adventures from an alternate universe. It would be really cool to see their reactions to different versions of themselves and the events that unfold.