Another possibility is a new, unknown enemy. This could be someone from a far - off land who has heard of Naruto's power and developed a special brainwashing jutsu just to take over Naruto and use him to conquer other villages.
Well, he could be made to do all sorts of things against his will. Maybe he'd be forced to fight his friends. It would be a really dark turn for his character, as Naruto is known for his strong will and loyalty.
In some fanfictions, the brainwashing jutsu on Naruto could be part of a bigger scheme. For example, a new villainous organization wants to use Naruto as a weapon. They brainwash him and try to control his immense power. But Naruto's willpower, even under the jutsu, might start to show through in small ways, and his friends use these glimmers to figure out how to save him.
Orochimaru is already a devious character. In Naruto mastermind fanfiction, he could be an even greater mastermind. He has vast knowledge of jutsu and forbidden techniques. He could be plotting to create a new world order by using his experiments and manipulating powerful ninja. He might even find a way to control the tailed beasts for his own ends.
Well, he could become extremely powerful. Maybe he'd use the forbidden jutsu to defeat powerful enemies like Madara or Kaguya in a really unexpected way. For example, if it was a time - travel related jutsu, he could go back in time and stop certain events from happening that led to the rise of these villains in the first place.
Perhaps with the help of his strong bonds with his friends. Their love and trust could be the key to snapping him out of it.
It could be Kabuto. He was always involved in sneaky and underhanded things. He might have created the spider spy to keep tabs on Naruto as part of Orochimaru's grand schemes.
Danzo could be a great mastermind in a fanfic. He was already a very shadowy figure in the original Naruto series, always plotting and scheming for the so - called greater good of the Leaf Village. In a fanfic, he could be the mastermind behind even more complex and devious plans, like secretly training a group of rogue ninjas to carry out his dirty work while maintaining his public image in the village.
He might learn a time - traveling jutsu. This would be really cool as it could allow him to go back and change certain events in the Naruto world, or gain knowledge from the past to use in the present battles.
Perhaps a new, unknown supervillain who has studied Captain America's weaknesses. This villain might be jealous of Captain America's status as a hero and decides to kidnap him to make a name for himself in the criminal underworld. He could be a brilliant strategist who plans every detail of the kidnapping carefully.
The mastermind behind Qingyu Nian was Wu Bo 'an. In the play, Si Lili and Wu Bo 'an conspired to assassinate Fan Xian and used the Second Prince's banquet to carry out the plan. In the prison, Fan Xian had used torture to force a confession and learned the identity of the mastermind from Si Lili. Therefore, Wu Bo 'an was confirmed to be the mastermind behind Si Lili.