Maybe an evil organization that is trying to disrupt the peace in the ninja world. They view Naruto and Sister Lemon as threats to their plans because of their combined strength and positive influence on the ninja community. Their leaders could be power - hungry individuals with a large army of minions at their disposal.
It could be a rogue ninja who has a vendetta against Naruto and sees Sister Lemon as an easy target to get to Naruto. This ninja might have some special powers that make him a formidable foe, like the ability to control shadows in a more sinister way than Naruto's shadow clone jutsu.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
It could be someone who also wants the power of the mask. Maybe a rogue ninja who has been researching the mask for a long time and sees Naruto as an obstacle to obtaining it.
Perhaps an ancient evil spirit that was sealed away long ago in Naruto's world but gets awakened by Ruby Lemon's presence. This spirit has the ability to possess people and use their skills for its own ends. It starts to cause chaos in the ninja villages and targets Ruby Lemon and Naruto specifically, seeing them as the key to either its complete destruction or its total domination.
It could be a new, self - made villain. Maybe a rogue ninja who was once rejected by the Hidden Leaf Village. He blames Naruto for his misfortunes and decides to target his sister as revenge. This villain would have his own set of unique and dangerous jutsu, which Naruto would have to figure out how to counter in order to save his sister.
Maybe an evil sorcerer from a third, unknown dimension who sees the potential in both Naruto's chakra and Pneuma's power. He plans to steal their powers to become invincible. He starts by creating unrest in both their worlds, pitting their friends and allies against them. Naruto and Pneuma must figure out his true identity and stop him before he succeeds in his devious plan.
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.
It could be a rogue member of Kara who has their own agenda and doesn't agree with any form of alliance with Naruto or the Hidden Leaf. This character might try to undermine any cooperation between Naruto and the rest of Kara.
Madara Uchiha could be a great antagonist. He could have somehow gained the power to cross into the Bleach universe and is causing trouble there. Yoruichi and Naruto would have to put aside their differences and combine their skills to stop him. Madara's powerful jutsu and his desire for power would make him a formidable foe for the duo.
It could be an organization of dark summoners. They believe that by sacrificing Matatabi, they can gain ultimate power. They send out their best agents to hunt down Matatabi and Naruto. These agents have the ability to manipulate dark chakra, which is harmful to both Naruto and Matatabi. The organization's leader is a powerful sorcerer who has been planning this for years.
It could be someone from a different ninja village who hears about the special jewelry that Naruto has. They send out their best agents, and Lemon could be working for them secretly. So, in this case, the main antagonist would be the leader of that ninja village who wants the jewelry at any cost, and Lemon is just a tool in their plan.