Perhaps an ancient being that was sealed away by the original Sage of Six Paths. It senses the presence of the fem Sage of Six Paths and Naruto and sees them as a way to break free. It manipulates other shinobi from the shadows, creating chaos and distrust among the villages, all while trying to get close to the duo to absorb their power and break the seals that hold it.
A good antagonist could be a rogue ninja who has somehow managed to gain some of the power of the Otsutsuki clan. He wants to use the fem Sage of Six Paths' connection to the origin of chakra to open a gateway to a world full of power that he can rule. He sees Naruto and the Sage as threats to his plan and constantly tries to sabotage their efforts to protect the world.
Maybe an ancient demon that was once sealed by the Sage of the Six Paths but has now been released. This demon could be bent on revenge and see Naruto, as the inheritor of the Sage's power, as its main target. It would be a formidable foe, with abilities that could test Naruto's new - found powers and his resolve. The demon could also corrupt other ninjas to do its bidding, creating more chaos in the ninja world.
Maybe it's a corrupted spirit from the avatar world that has become jealous of Naruto's unique powers as the Sage of Six Paths. This spirit could try to possess Naruto or those close to him in order to gain access to his powers and use them to rule over both the Naruto and avatar universes. It would be a very powerful and menacing antagonist as it can manipulate the elements in the avatar world and has knowledge of Naruto's world through its research on him.
Perhaps an ancient demon that was sealed away by the original Sage of Six Paths is reawakening. This demon, having been dormant for so long, is extremely powerful and wants revenge on the world that the Sage of Six Paths helped create. It would see Naruto, as the reborn Sage, as the main obstacle in its path of destruction.
It could be Voldemort still. Even with Harry having the powers of the Sage of Six Paths, Voldemort would be a formidable foe. He might be intrigued by this new power and try to steal it for himself.
Maybe the fem Sage of Six Paths is reincarnated in the modern era of Naruto's world. Naruto is initially skeptical but soon realizes her power and knowledge. She reveals that there is a prophecy about them working together to bring about a new era of peace. So, they start training the new generation of shinobi together, combining their different styles and teachings, which also leads to some romantic undertones between them.
Kaguya could be a great antagonist. Even though she was sealed away, in a fanfiction, she could break free and seek revenge. Her power level is extremely high, and she has a deep understanding of the Sage of Six Paths Senjutsu, which would make her a formidable foe for Naruto.
Yes, in some fanfictions, Naruto is depicted as the Sage of the Six Paths. Fanfiction writers often like to create alternate storylines where Naruto attains this powerful status. It gives them the freedom to explore different aspects of Naruto's character and the Naruto universe in a new and exciting way.
Obviously, Naruto is the main character since it's about him being the Sage of Six Paths. But other characters like Sasuke are often important too. Sasuke might be Naruto's ally or sometimes a rival even with Naruto's new status.
Hinata could also be a main character. Her relationship with Naruto could take on new dimensions as he becomes the Sage of Six Paths. Maybe she helps him in some way to control or understand his new powers, or they face challenges together that test their relationship.
It could entail Naruto having new and more powerful forms. For example, his Sage Mode could be enhanced with Six Paths chakra, giving him abilities like instant teleportation across great distances or the power to nullify any jutsu with a simple touch.