One idea could be that Amy initially sees Metal Sonic as a threat but then realizes he has some sort of glitched 'conscience' and tries to help him. For example, she might notice that he is being controlled against his will in a way and tries to free him from that control.
For Amy, she could become more understanding of the 'evil' or opposing side. Instead of just seeing Metal Sonic as a bad guy, she might learn to look deeper into his existence as a creation. This could make her more empathetic in general.
One interesting plot could be that Metal Sonic is damaged and Amy, out of her kind heart, tries to fix him. As she does, she starts to understand him more and they form an unexpected bond. This challenges her feelings for Sonic as she sees a different side of a robotic version of him.
In some fanfictions, Sonic and Amy's pregnancy could be a result of a magical accident. They then have to learn how to be parents quickly. Sonic, who is used to being on the go all the time, has to slow down and be more responsible. Amy, on the other hand, is overjoyed but also a bit worried about how Sonic will adjust. They both grow closer as they prepare for the arrival of their baby.
One idea could be that Sonic and Amy face challenges in preparing for the baby while still dealing with their usual adventures. For example, Sonic might have to slow down a bit, which is really hard for him as he's always on the go. Another plot could be that their friends in the Sonic universe all come together to help them get ready, like Tails building special baby gear.
A plot could be where Amy discovers a prophecy about Dark Super Sonic being the key to saving their world from a greater threat. So, she decides to follow him around and tries to understand his powers. As she does this, they form an unlikely bond. Along the way, they face various challenges together, and Amy's love for Sonic (even in his dark form) might be the driving force that helps them overcome all the difficulties.
A plot could involve Amy Rose being turned into a different form by the magic in the Black Knight's world. Sonic then has to find a way to reverse it. Along the way, they encounter various characters from the Sonic and the Black Knight game, and together they must face a new, powerful enemy that threatens the entire realm.
One idea could be that Amy and Jake have to solve a mystery in their neighborhood. They could start by interviewing neighbors and finding strange clues. Another could be a time - travel plot where they end up in a different era and have to adapt while still maintaining their relationship. Maybe they could also go on an undercover mission together where they have to pretend to be a different couple to catch a criminal.
A story could revolve around Sonic and Elise finding a magical object. This object has the power to change the balance in Sonic's world. They have to decide what to do with it. Elise, with her gentle nature, might want to use it for peaceful purposes, while Sonic is more concerned about the potential misuse by his enemies. They have to work together to figure out the best solution, which could lead to a lot of character development and exploration of their relationship.
Another plot could involve Antoine having to team up with an unlikely character. For example, he teams up with a villain who has a change of heart temporarily. Together they face a greater threat that endangers the whole Sonic universe. This would create an interesting dynamic between them as they learn to trust each other.
One good Metal Sonic x Amy fanfiction could be 'A Strange Bond'. It explores an alternate universe where Metal Sonic has a malfunction that makes him see Amy in a different light. He starts to protect her instead of being an enemy. Another one might be 'Unlikely Affection' which delves into how Amy's kindness slowly chips away at Metal Sonic's cold, robotic exterior. There's also 'Metal Hearts' that focuses on a journey of self - discovery for both characters as they interact in unexpected ways.