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.
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.
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.
There could be new original antagonists created specifically for the fanfiction. These might be dark entities that are related to the source of Dark Sonic's power, trying to either control him or use his power to spread chaos in Sonic's world.
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.
I'm not entirely sure specifically what 'sonic brainwashed fanfiction' is about without reading it. It could be a fan - made story within the Sonic the Hedgehog fandom where a character is brainwashed in some way. Maybe Sonic himself gets brainwashed and the story explores the consequences and how other characters deal with it.
I'm not aware of any extremely popular 'sonic brainwashed fanfiction' works specifically. There are so many Sonic fanfictions out there that it's hard to single out ones with this particular theme as being overly popular.
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.
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 possible main antagonist could be an ancient evil that has been awakened by the discovery of the Dark Excalibur. This entity might be seeking to use Sonic as a pawn to spread chaos and destruction. For example, it could be a long - forgotten dark wizard who once forged the Excalibur for evil purposes.
One possible main antagonist could be Dr. Robotnik's sister, who is even more devious and has a different set of robotic creations. She could be jealous of Sonic's speed and popularity and wants to take over the world just like her brother, but with her own style.