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.
Link would likely be a bit of an enigma to the Avengers at first. He doesn't talk much but his actions would speak volumes. He'd probably be very respectful of their powers but also not shy about showing off his own skills when necessary. For example, during a fight, he could quickly adapt to the Avengers' fighting style and work with them in a seamless way, like how he teams up with different characters in his own games.
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.
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 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.
One idea could be that Godzilla is drawn to the energy source of one of the Avengers' tech, like Stark's Arc Reactor. This causes chaos as Godzilla approaches the city where the Avengers are based. The Avengers initially see Godzilla as a threat and try to fight it. But then they realize that an even bigger alien force is using Godzilla's presence as a distraction. So, they have to find a way to communicate with Godzilla and work together to defeat the common enemy.
One idea could be that Nightwing is transported to the Avengers' universe through some sort of interdimensional rift. He then has to team up with the Avengers to fight a common enemy, like Thanos who has somehow acquired some of Batman's tech. Nightwing's acrobatic skills and detective abilities would be a great addition to the Avengers' power set.
A crossover could involve the magic systems. Zelda has its own brand of magic, and Skyrim has a complex magic system too. Maybe a mage in Skyrim discovers a way to open a portal to Hyrule and brings back some magic items or spells. This could cause chaos as the two different magics interact in unexpected ways. The dragons in Skyrim might be interested in the new magic, leading to some epic battles.
One more theme is the exploration of different moralities. The relatively simple good - vs - evil in Hyrule is contrasted with the more complex moral landscape of the DC Universe. This can lead to some interesting internal struggles for the characters as they navigate these different moral frameworks and try to figure out who the real enemies are and who can be trusted.