One idea could be that Link, the hero from Legend of Zelda, somehow gets transported to the world of MLP. He might team up with Twilight Sparkle to fight against a common enemy that threatens both their worlds. Maybe Ganon has found a way to corrupt the magic in Equestria, and Link's combat skills along with Twilight's magic knowledge are needed to stop him.
Another interesting concept is to have Zelda herself be turned into a pony. She could use her wisdom to help the ponies in Equestria solve complex problems. For example, she could assist in finding a solution to a drought that is affecting the land by using her understanding of ancient magic, which could be similar to the magic in the MLP world but with a different twist.
A fun scenario could be that the Triforce from Legend of Zelda has fragments that end up scattered across Equestria. The ponies, not fully understanding what it is, start having strange things happen around them. The main characters from MLP then team up with characters like Link or other Zelda - related characters to find and reunite the Triforce fragments before they cause chaos in both worlds.
It could be about Link ending up in Equestria and teaming up with Twilight Sparkle to fight a new evil that threatens both their worlds. Maybe Ganondorf has found a way to enter Equestria and is causing chaos, and Link uses his combat skills while Twilight uses her magic to drive him out.
Another concept could be that some of the magical creatures from Harry Potter end up in the Zelda world. Hippogriffs could be used as a form of transportation for Link and his allies. And the house - elves could have an interesting role, perhaps they help out in the various villages in the Zelda world, using their magic to clean up and cook, while also getting a taste of freedom in this new world.
One idea could be Link crossing over into a modern world. He'd be confused by the technology like cars and cell phones. Another could be Link teaming up with a character from another game, like Mario. They could combine their skills to defeat a common enemy.
Maybe Zelda herself could be transported to the Avengers universe. With her wisdom and magic, she could assist the Avengers in different ways. She could use her magic to heal the wounded Avengers or help Tony Stark understand some ancient technology that has similarities to her own world's tech. She could also provide strategic advice based on her experience dealing with Ganon in her own realm.
One idea could be that Link, from Legend of Zelda, somehow gets transported to the Naruto universe. He might initially be mistaken for a strange shinobi with his unique green tunic and hat. Link could use his combat skills, like swordsmanship and shield defense, to team up with Naruto and his friends against common enemies, such as the Akatsuki who are after powerful artifacts. Maybe the Ocarina of Time has some sort of power that the Akatsuki wants, and Link has to protect it while in this new world.
Some great Legend of Zelda crossover fanfiction concepts include a crossover with the Sonic the Hedgehog series. Link could be racing through the Green Hills Zone on Epona. A crossover with the Super Mario Bros. universe is also a fun idea. Link and Mario could join forces to rescue Princess Zelda and Princess Peach from the clutches of their respective villains. Additionally, a crossover with the Kingdom Hearts series would be epic. Link could interact with Sora and the other Keyblade wielders, exploring different Disney and Zelda worlds together.
The characters could interact through shared quests. For instance, if there's a dark force emerging in both worlds, they might work together to defeat it. Link could teach the ponies some combat skills like sword - fighting (maybe in a pony - friendly way), and the ponies could teach Link about their unique magic and how it works in Equestria.
Link and Twilight Sparkle would be obvious main characters. Link with his skills in combat and exploration, and Twilight Sparkle with her powerful magic and intelligence. They could form an unlikely duo to face challenges.
A great idea for a BotW fanfiction could be a 'what if' scenario. For example, what if Link failed to defeat Calamity Ganon? You could write about how Hyrule is plunged into even deeper despair, and how the remaining survivors, including Zelda, try to fight back. Or perhaps a story centered around the different races of Hyrule working together to build a new city, away from the ruins of the old Hyrule Castle. This could explore their relationships and how they combine their unique skills.
One idea could be that Naruto and Link swap worlds. Naruto finds himself in Hyrule and has to figure out how to use the Master Sword while Link ends up in the Ninja world and tries to learn chakra control and ninjutsu. Another idea is a combined quest where characters from both universes team up to defeat a common enemy, like a powerful dark sorcerer who is causing chaos in both the Elemental Nations and Hyrule.