It could be an evil ninja who has somehow gained access to the technology from Neo's world and wants to use it to take over the Naruto world. He might be able to create clones using digital technology, making him a very difficult enemy to defeat.
One possible plot could be that Naruto somehow gets transported to the RWBY universe. He teams up with Neo. Maybe they start off as rivals, with Neo being distrustful of Naruto at first because of his strange powers. But as they face common enemies, like the Grimm in the RWBY world, they learn to work together and combine their unique abilities, like Naruto's jutsu and Neo's semblance.
Perhaps Neo could teach Naruto about the concept of the digital world, which Naruto then uses to create a new form of jutsu. Meanwhile, Naruto could show Neo the power of friendship and teamwork in the ninja way, changing Neo's perspective on fighting.
It could be a combination of villains from both universes. For example, Orochimaru from Naruto could team up with Salem from RWBY. Orochimaru is interested in the power of the Grimm and Salem wants to learn about the power of chakra. Their combined evil could be a huge threat to Naruto and Neo, forcing them to use all their skills to defeat this powerful alliance.
One common theme is friendship. Despite their differences, Neo and Ruby often form a bond in these fanfics. Another theme is self - discovery. As they interact, both characters learn more about themselves.
One common theme is redemption. For example, Cinder might be on a path to redeem herself and Neo could play a part in that journey. Another theme is friendship or an unlikely alliance. They are from different backgrounds and having them form a bond is an interesting exploration.
One main theme is mentorship. Neo Yondaime often acts as a mentor to Naruto, guiding him in his ninja path. Another theme is legacy. It explores how Neo Yondaime's legacy impacts Naruto and the ninja world. And there's also the theme of friendship. Despite their differences in status and power, they form a bond of friendship.
One idea could be a story where Naruto is transported to the Matrix world where Neo exists. He could use his ninja skills to fight against the Agents in a new and unique way. Maybe he teams up with Neo and they learn from each other's combat styles.
It could be a rogue shinobi who has found a way to enter the Matrix world and wants to take over both the real world and the Matrix. He uses his ninja techniques combined with the power of the Machines to create havoc.