Well, they can keep Sonic's core values intact. For example, Sonic has always been about freedom and justice. Even with amnesia, he could still show a natural inclination towards helping those in need. Maybe he doesn't remember why he does it, but he just feels it's the right thing to do.
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.
I'm not sure specifically as there could be various interpretations in such a fanfiction. Maybe Metal Sonic sets Sonic up in a way that makes Sonic look bad to the other characters, perhaps by faking some evidence or causing chaos and making it seem like Sonic's fault.
Positive Sonic fanfiction could be about Sonic mentoring the younger characters like Tails and teaching them important life lessons. Or it could be about Sonic and his friends having to solve a mystery in their world, like a strange disappearance of an important item or character. Fanfictions that show the characters growing and evolving in positive ways, such as Amy becoming more confident in her own abilities, are also excellent alternatives to inappropriate fanfiction themes.
Sonic would probably be very shocked at first. He trusts Amy, so her betrayal would be unexpected. He might initially try to talk to her to understand why she did it.
It could be Dr. Eggman. He's always been after Sonic and trying to defeat him. Experimenting on Sonic could be his new way to find Sonic's weaknesses or to gain his powers for himself.
I'm not entirely sure specifically as there could be many interpretations. It might be a fanfiction where Sonic, the character, experiences some sort of 'breaking' event. Maybe he gets injured, or his spirit is broken in some story - created - by fans.
Well, in this 'sonic gets roboticized fanfiction', it might explore the idea of Sonic's identity when he becomes robotic. It could show how his friends react to this new form. For example, Tails might be shocked at first but then try to find a way to reverse the roboticization. And Sonic himself could be struggling with feeling less 'alive' in his robotic state, all while facing new enemies or challenges that are related to his new robotic nature.
Yes, there might be some fan - created stories that explore unique and family - friendly concepts related to Sonic characters in a fictional pregnancy scenario. However, it's important to note that these are often in the realm of creative fan interpretations.