Another possibility is that Godzilla somehow ends up in the Naruto world. The shinobi might initially see it as a great threat, but Naruto could try to communicate with it using his ability to sense emotions. Maybe Godzilla is there because it's being chased by an even greater enemy from its own world, and Naruto and his friends decide to help it.
A more creative fanfiction idea could be a fusion of Naruto and Godzilla's powers. A character in the Naruto universe could gain Godzilla - like powers, perhaps through some strange experiment or ancient curse. Naruto would then have to deal with this new, powerful and unpredictable foe while also trying to find a way to reverse the transformation.
One idea could be that Naruto is transported to the Godzilla universe. He could use his ninja skills to try and communicate with Godzilla or other kaiju. Maybe he'd attempt to use his shadow clone jutsu to confuse the monsters during a battle.
A possible fanfiction could involve Kiryu's memories of Godzilla influencing the RWBY characters. For example, Godzilla's tenacity and will to protect could inspire Ruby and her team. They could learn from Kiryu's combat techniques and use them against the Grimm. And perhaps Kiryu could be repaired and upgraded using RWBY's technology.
Perhaps a dark wizard uses magic to create an Animagus - Godzilla hybrid as a weapon. The Harry Potter gang has to find a way to stop this abomination. They might use their own Animagus forms to combat it. For example, Harry could turn into his stag Animagus and use its speed and agility to distract the Godzilla - Animagus while Hermione figures out a spell to reverse the dark magic.
In some fanfiction, Godzilla could be a guardian of a hidden magical realm within the Harry Potter universe. This realm contains powerful magic that could be used for good or evil. Voldemort tries to gain access to this realm to get more power, but Godzilla stands in his way. Harry and his friends then have to decide whether to help Godzilla protect the realm or try to find a way to use the power within for their own fight against Voldemort.
One idea could be to have characters from Naruto end up in the world of Danmachi. For example, Naruto himself could find his way into the dungeon and his ninja skills would be put to the test against the dungeon monsters. His shadow clone jutsu could be used in interesting ways, like sending clones into different dungeon levels to scout or fight. Another idea is to have the concept of chakra introduced into the Danmachi world. This could change the way adventurers fight and level up. Maybe some of the Naruto characters could train the Danmachi adventurers in new combat techniques.
One idea could be a crossover where Naruto is somehow transported to the Star Wars universe and meets Padme. Maybe he uses his ninja skills to protect her from the Sith.
Another concept is that Naruto is sent to Middle - earth. There, he could use his ninja skills and chakra powers. He and Gandalf could team up to fight Sauron. Naruto's ability to make friends and inspire others would be really useful in uniting the different races of Middle - earth against the common enemy.
A more complex idea is that the Matrix is used to create a virtual training ground for the shinobi. They enter the Matrix to practice their skills in a more controlled environment. However, they soon realize that there are some dark secrets within the Matrix, and Naruto has to lead the way to uncover the truth and free those who are trapped inside.
Another possibility is that Naruto visits the Townsville, the city where the PPG live. He might be confused by the modern technology there compared to his own world. The PPG could teach him about it while he shows them some of his ninja skills like tree - climbing and water - walking.
A third idea could be a story where Naruto's clones are mistaken for some kind of superpower by the Thundermans. Max might be intrigued and try to figure out how to do it himself. Meanwhile, the Thundermans could teach Naruto about modern technology which he has never seen in his own world. This could lead to some really interesting and comical situations as they try to understand each other's worlds.