It could be a rogue ninja from a forgotten clan who wants to steal the unique powers of Naruto, Naruko, and Satsuki. He sees their combined potential as a threat to his own evil plans of taking over the ninja world. This antagonist might have some ancient and powerful jutsu that the three heroes have to figure out how to counter.
One common theme is friendship. They all grew up in the same village and have different relationships with each other. Fanfictions might explore how they support each other through tough times. For example, during a difficult mission.
Maybe a fanfiction where they are all in a different timeline. Naruto and Naruko are from a more peaceful Konoha, and Satsuki has been sent there as an ambassador of sorts from her village. At first, there are misunderstandings, but as they get to know each other better, they start to work together to improve relations between their villages. They learn from each other's cultures and ninjutsu techniques, creating a unique bond.
It could be an evil scientist who created the clones for his own malicious purposes. He might want to use their power to take over the Hidden Leaf Village. This antagonist would constantly be trying to control the clones and use them as weapons.
Maybe an evil organization that wants to use Naruto's power and the connection he has with Kushina for their own dark purposes. They see Natsumi as an obstacle in their plan because she is always by Naruto's side. This organization could be experimenting with dark jutsu and need Naruto's chakra and Kushina's latent abilities (passed on to Naruto) to complete their evil experiments.
Well, one great place to start looking for such fanfictions is on Archive of Our Own (AO3). There are numerous stories there. Some might focus on their adventures together in a new mission that wasn't in the original series. Another might explore their relationships in a more slice - of - life setting, like them just hanging out in Konoha.
One option could be Kaguya from the Naruto universe. Her god - like powers would pose a great threat to Bayonetta. She could be trying to expand her influence into Bayonetta's world, seeing it as a new place to conquer.
It could be a dark wizard who wants to capture the nymph for her powers. He sees the nymph's connection to nature and wants to use it to gain ultimate power in the Naruto world.
It could be a rogue ninja who has also discovered a way to harness the power of Amaterasu in a corrupt way. This ninja might want to use the power to take over the ninja villages and Naruto stands in his way.
It could be an evil ninja from Naruto's world who has somehow gained the ability to control Digimon. He wants to use this power to rule over both worlds. He targets Renamon because of her connection to Naruto and tries to break their bond. He might also be after the special powers that Naruto and Renamon possess when they work together.
It could be a rogue ninja who has a vendetta against Naruto and sees Heather as a way to get to him. Maybe this ninja was once defeated by Naruto and now wants to use Heather as bait or hurt her to break Naruto's spirit.