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.
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.
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 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.
In 'sonic gets hypnotized fanfiction', a prevalent theme could be the exploration of Sonic's mind. How does the hypnosis affect his thoughts, memories, and actions? Another theme might be the power dynamics. The one who hypnotizes Sonic has a certain power over him, and this can create tension and conflict. Additionally, the fanfiction may touch on themes of friendship as Sonic's friends come to his rescue and try to break the hypnosis.
One common theme is trust. When Sonic is betrayed, it shatters the trust he had in his friends or allies. This often leads to a journey of rebuilding that trust or finding new trustworthy companions.
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.
Common themes might revolve around the challenges the character faces. For instance, dealing with physical changes in a world where Sonic characters are usually more focused on speed and adventure. There could also be themes related to the future. How will the pregnancy change the character's future and the future of the Sonic universe? Additionally, themes of love and care might be prominent as the character navigates this new phase, whether it's the love for an unborn or the care from friends and family.