Some fanfictions might feature a new, powerful and mysterious enemy as the one who brainwashes Naruto. This character could be from a far - off land with unique powers. They might target Naruto because of his status as a jinchuriki and his potential to change the balance of power in the ninja world.
Orochimaru is often a common antagonist in these types of fanfictions. He has a history of experimenting on people and his knowledge of jutsu could be used to brainwash Naruto. He might want to use Naruto's power for his own evil plans.
Eggman is by far the most common antagonist in these fanfictions. He has the motive and the means to brainwash Sonic. He's always looking for ways to defeat Sonic and gain control over the Chaos Emeralds, so using brainwashing technology on Sonic fits right into his evil plans.
The Akatsuki could be likely antagonists. They are always interested in powerful ninja like Naruto. They might use some forbidden jutsu to control Naruto to further their goals of collecting the tailed beasts. Another possibility is Orochimaru. He is always looking for ways to gain power and Naruto's power would be very appealing. He could try to control Naruto to use him in his experiments or to fight his enemies for him.
One common plot could be Sonic being brainwashed by a powerful villain like Eggman. The villain might use some new high - tech device to control Sonic's mind. Then Sonic starts to do things that are against his friends and nature, like attacking Tails or helping Eggman steal the Chaos Emeralds. Another plot could involve an alien force brainwashing Sonic and using him to open a portal to their world for invasion purposes.
In some fanfictions, Naruto is brainwashed to believe he is from another village. So he starts working for their goals. This could lead to a lot of interesting interactions as he clashes with his former comrades. The story might explore how he slowly starts to remember his true identity through small flashbacks and the bonds he has with his friends.
Hawkmoth is usually the main antagonist. Since he is the one who akumatizes Marinette in the first place. He takes advantage of her negative emotions, like her insecurities or anger, to turn her into an akuma and use her for his own evil plans.
Sasuke can often be an antagonist in these types of fanfictions. Since Sasuke is also power - hungry in the original series, he and Naruto's quests for power could put them at odds. Their rivalry could be intensified as Naruto becomes more and more obsessed with power, leading to some epic battles between them.
Often, ancient and powerful demons or dark gods can be antagonists. They might see Naruto's newfound godhood as a threat to their own power or plans. For example, a demon that has been sealed away for centuries could be awakened by Naruto's ascension and seek to destroy him.
Well, often there could be themes of power struggle. Maybe a character gets brainwashed to do things against their will in the Naruto universe. And it might involve some altered relationships due to the brainwashing.
Pain is often one of the main antagonists. Since in the original story, Pain was the one who ultimately killed Jiraiya. So in fanfictions where Naruto saves Jiraiya, Pain is a natural choice to be the bad guy. Another common antagonist could be Orochimaru. He had his own vendetta against Jiraiya and the Hidden Leaf Village. He might be trying to use Jiraiya for some evil experiment or to gain access to the secrets of the Sage Mode.
Maybe the hidden organizations within Konoha that work in the shadows. They could have been involved in some plot against Naruto that led to his decision for revenge. They would be the ones trying to stop Naruto from exposing their secrets and exacting his revenge on the village as a whole.