Another idea is that Zelda characters find themselves in the Naruto world. They could get involved in the ninja academy and learn about chakra. Maybe Zelda herself could try to master some of the ninja arts and use her magic in combination with it. This would lead to a lot of interesting interactions between the Zelda characters and the ninja students.
A third plot idea might be that a group of Naruto characters accidentally end up in the Zelda world. They team up with the local heroes to stop Ganon from getting his hands on some powerful ninja artifacts. Along the way, they discover similarities between their own powers and the magic in the Zelda world. This could involve Naruto using his shadow clones to outwit Ganon's minions while Link uses his combat skills to take on the tougher foes.
One idea could be a story where a young Bokoblin gets separated from its pack and is found by Zelda. Instead of harming it, Zelda tries to teach it kindness and cooperation. The Bokoblin could then become an ally to Zelda, helping her understand the ways of the Bokoblins better, and they could work together to solve some problems in the Zelda universe, like finding a way to stop a natural disaster threatening Hyrule.
One plot idea could be a training arc. Naruto could teach Illya some basic ninja skills like stealth or tree - climbing, while Illya could show Naruto some of her magic spells for defense. Another idea is a mystery - solving plot where they team up to figure out why strange things are happening in both their worlds. For example, strange creatures are appearing in Konoha and in Illya's town that seem to be related.
One plot idea could be a female Sasuke who uses her unique skills in a different way than the male Sasuke in the original. For example, she might focus more on diplomatic solutions to problems in the ninja world, using her intelligence and combat skills to broker peace treaties.
One plot idea could be that Naruto gets transported to the world of Equestria. Princess Celestia senses his strange power and they start to communicate. Naruto helps the ponies in Equestria deal with a new threat using his ninja skills, and in return, the ponies teach him about their magic. It could be a story of friendship and cultural exchange.
A plot could also be where Naruto is wrongly accused of being a succubus - like being a danger to the village because of some strange powers he has. Kushina, even though she has passed away, appears to Naruto in his mind or as a spirit guide. She gives him the strength and wisdom to prove his innocence and show that his powers can be used for good, rather than being seen as something evil like a succubus.
Perhaps in this fanfiction, Naruto and Korra find themselves in a situation where their pregnancies are part of a prophecy. They then have to figure out how to fulfill the prophecy while dealing with the normal challenges of pregnancy like mood swings and physical discomfort. They could meet other characters from their respective universes who help them on this journey, like Kakashi guiding Naruto on how to be a good father - to - be and Tenzin giving Korra advice on handling her new situation.
One idea could be that Naruto and Captain Marvel are brought together by some sort of interdimensional rift. They have to figure out how to get back to their respective worlds while also dealing with threats in the new world they are in. Maybe they have to combine their powers, like Naruto's shadow clones and Captain Marvel's energy blasts, to defeat a powerful villain.
One idea could be that the clone has unique abilities that Naruto doesn't have, and they work together to develop new jutsu. For example, the clone might have a special connection to nature chakra that Naruto can learn from.
One plot idea could be that the female Kurama helps Naruto in a different way than in the original story. For example, she could use her unique chakra to teach Naruto a new jutsu that is crucial for a major battle against a new enemy. And their relationship could be more of a mentor - mentee kind of bond.
One plot idea could be that Naruto and Temari are forced into an arranged marriage for political reasons between their villages. Over time, they start to understand each other better and develop real feelings. Then, through some magical or medical miracle, Temari becomes pregnant. Another idea is that they go on a dangerous mission together, get separated from their teams, and during that time, they make a deep emotional connection which leads to Temari getting pregnant later on in a very natural and story - appropriate way.