Another possible antagonist could be a rogue Uchiha. One who didn't agree with Shisui's views on peace. This rogue Uchiha could see Naruto as an outsider interfering with Uchiha matters and Shisui as a traitor for teaming up with Naruto. So they set out to disrupt their partnership and cause chaos in the village.
Maybe it's an ancient evil that has been awakened. It targets both Naruto and Konan because of their unique powers. The evil being could be trying to use their powers to break free from a long - held seal. So, Naruto and Konan have to put aside their differences and fight this powerful foe together.
It could be a jealous gamer who is envious of Naruko's skills and Naruto's natural talent. This antagonist might try to sabotage their progress in the game by hacking or spreading false rumors within the gaming community in the fanfic.
A group of rogue demigods could be the antagonists. They are jealous of Percy and Jason's fame and power. They form a secret alliance and start causing trouble for the other demigods. Percy and Jason meet while trying to figure out who is behind these attacks. At first, they suspect each other, but then they realize the real culprits are this group of rogue demigods and join forces to stop them.
One possible plot could be that Naruto accidentally travels back in time and meets Shisui. Shisui, seeing Naruto's potential, decides to train him in some of his unique jutsu. This would give Naruto an edge in his future battles and also a new perspective on the Uchiha clan.
Maybe a rogue ninja who has somehow tapped into dark powers related to Kami's domain. This ninja wants to use these powers to take over the ninja world, and Naruto, with Kami's help, has to stop him. In this fanfiction, the rogue ninja could have some personal vendetta against Kami as well, which adds more depth to the story.
It could be an ancient evil that Rikudou Sennin once sealed away. With Naruto and Rikudou Sennin meeting, this evil might sense an opportunity to break free and becomes the antagonist.
It could be an evil shinobi who wants to disrupt the meeting between Naruto and Kushina. Maybe they know that Kushina has some special knowledge or power that she could pass on to Naruto, and they don't want that to happen.
It could be a rogue Sound ninja who has his own agenda. Maybe he wants to start a war between Konoha and the Sound Village to gain power in the chaos. He would see Naruto as a threat to his plans and try to eliminate him.
It could be Voldemort who somehow manages to cross over into the Star Wars universe. He might see the power of the Force as something to be harnessed for his own evil purposes. His dark magic would be a great contrast to the light - side teachings of Yoda, and Harry and Yoda would have to team up to stop him.
Lex Luthor could be an interesting antagonist in this scenario. He could be using his intelligence and resources to create a weapon that could neutralize both Batman and Wonder Woman. He might be working with some of Batman's rogues gallery or even some of Wonder Woman's enemies. His presence would add a different dynamic as he's a human villain but with extraordinary cunning and resources.