Another possibility is that a Naruto character with Mokuton abilities is transported to the RWBY world. This character could then teach some of the RWBY characters about chakra and how to use Mokuton. It could lead to new battle strategies and team-ups in the RWBY world.
A more complex fanfiction could involve the origin of Mokuton being related to the Dust in RWBY. For example, there could be a hidden connection between the two that was lost in time. A group of characters from both universes could go on a quest to discover this connection and in the process, combine their powers in unexpected ways.
One idea could be a crossover where a character from RWBY discovers the ability to use Mokuton. They might struggle at first to control it, like Naruto did. Maybe they could use it to create unique weapons or defenses in the RWBY universe.
One idea could be a story where a new character is born with the unique combination of Rinnegan, Sharingan and Mokuton abilities. This character could struggle with the power and the attention it brings from different ninja clans. They might be seen as a threat or a savior, depending on who's looking at them.
Another possibility is a story in which a character from RWBY is sent to the Naruto world and then later ends up in the Overwatch universe. They could bring their unique combat style and start training with the different groups in each world, like learning ninjutsu in Naruto and using advanced tech in Overwatch.
One idea could be a crossover where Cinder somehow gets transported to the Naruto universe. She might initially try to use her powers to gain control, but then realizes she has to adapt to the new chakra - based powers. Meanwhile, RWBY characters could also end up in the Naruto world in search of Cinder and end up forming unexpected alliances with Naruto and his friends.
A possible fanfiction could be about the origin of the Rinne Sharingan having some connection to the world of RWBY. Maybe there was an ancient civilization in RWBY's past that had a similar power, and through some sort of dimensional rift, it influenced the development of the Rinne Sharingan in Naruto's world. This would involve a lot of world - building and exploration of both universes' histories.
One idea could be a crossover where Naruto, with his Mokuton abilities, somehow ends up in the Avatar universe and meets Azula. Maybe he tries to use his Mokuton to counter her firebending in a big battle. Another could be a story where Azula discovers a way to use Mokuton-like powers through some dark magic and Naruto has to stop her from misusing it.
In a fanfiction, what if a Sharingan user discovers a way to transplant Mokuton cells into their body to gain the ability? However, they soon realize that the combination is not as easy to control as they thought. The Mokuton starts to take over their body, and they have to find a way to either master it or reverse the process. They might seek help from old allies of Naruto or explore ancient ninja scrolls for a solution.
It could be really exciting. Imagine Percy Jackson using Naruto's Mokuton abilities in the world of Greek mythology. He could create wooden structures to help him in battles against monsters. For example, he could make a wooden shield or a tower to hide behind when facing a powerful foe like a Cyclops. The combination of the two different fictional elements would bring a whole new level of creativity to the story.
One idea could be to have the characters from RWBY travel through a stargate to the Pegasus Galaxy where Stargate Atlantis is located. They could encounter the Wraith and have to use their unique abilities from Remnant to fight them. For example, Ruby's speed and Crescent Rose could be very useful in combat against the Wraith.
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.
One idea could be that Captain America is somehow transported to the RWBY universe. He could team up with Team RWBY to fight against the Grimm. His shield would be a unique weapon in that world, and his leadership and combat skills would be highly valuable.