A power - hungry clan leader might be the antagonist. They discover the existence of the Star Sage's power and believe it can make their clan the most powerful in the Naruto world. So, they start a quest to obtain it, regardless of the destruction it may cause, and the main characters have to stop them.
Perhaps an ancient demon that was sealed by the Star Sage long ago has now broken free and is seeking revenge. It sees the descendants of the Star Sage as a threat and tries to eliminate them one by one. The main characters then have to find a way to defeat this demon using the limited knowledge they have about the Star Sage.
It could be a rogue ninja who was once rejected from the lightning sage training and now wants to destroy the entire concept of the lightning sage. He might have developed his own dark lightning - based techniques to oppose the traditional ones.
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.
It could be a power - hungry shinobi within Kiri. This shinobi might see the Sage as a threat to his own rise in the village hierarchy. So, he uses his influence to keep the Sage neglected and also tries to sabotage any attempts by the Sage to gain recognition.
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.
Darth Maul could be a great antagonist. His double - bladed lightsaber would be a formidable weapon against Naruto. Maul's acrobatic fighting style and his Sith powers would pose a huge challenge to Naruto's ninja skills and new - found Jedi powers.
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.
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.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
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.