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.
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.
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.
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.
One interesting plot could be Sonic forgetting who his friends are. His friends then have to re - introduce themselves and remind him of all the good times they've had together. For example, Tails could show Sonic their workshop and all the inventions they made together, gradually triggering Sonic's memories.
One possible plot could be that Sonic is bullied by a new group of antagonists in his world. They might make fun of his speed, saying it's not all that great and constantly tripping him up during races. Another plot could be that Sonic is bullied by some of the other characters who are jealous of his popularity. They start spreading false rumors about him, which makes some of the animals in the forest start to avoid him.
One possible plot could be Sonic being framed for stealing the Chaos Emeralds. He then has to go on a journey to prove his innocence while facing his friends who have turned against him.
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 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.
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.
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.