One possible plot could be that Amy Rose discovers her closest friend has been secretly working against her goals. For example, if she's on a mission to save Sonic, and she finds out that someone she trusted has been trying to undermine her efforts all along. This could lead to her feeling betrayed and having to re - evaluate all her relationships.
Maybe in the fanfic, Amy Rose is betrayed by her love interest. Suppose she thought Sonic was in love with her too, but then she finds out he has been using her feelings to get something else, like access to a powerful artifact she was guarding. This would be a huge betrayal for her, shattering her romantic dreams and making her question her own judgment.
Even one of her friends like Tails could be the betrayer in a really unexpected plot twist. Maybe Tails is forced to betray her by some external threat. For example, if an enemy captures Tails and threatens to harm him or Sonic if he doesn't give away some important information about Amy Rose or lead her into a trap.
Well, in a 'mikan sakura betrayed fanfic', she could be betrayed by her family. Say her sister steals an important opportunity from her, like a chance to study abroad or participate in a big competition. It would be a huge betrayal as family is supposed to support each other. Also, in a magical or fantasy version, Mikan could be betrayed by her mentor in the art of magic. The mentor might use Mikan's trust to steal a powerful magical artifact that Mikan was supposed to protect.
It could be that the whole Team 7 is brainwashed by an evil ninja with powerful genjutsu abilities. They are made to believe that Naruto is the key to a great evil that will destroy the ninja world. As a result, they turn on Naruto, and he has to fight not only his former teammates but also the false accusations and the real threat behind the brainwashing.
One possible plot could be that Konoha's leaders, fearing Naruto's growing power, secretly plan to get rid of him. They spread false rumors about him, turning some of the villagers against him. Another plot might be that they frame Naruto for a crime he didn't commit, perhaps a major attack on the village, in order to justify exiling or imprisoning him. A third possibility is that they withhold important information from Naruto that could put his life in danger, all in the name of protecting the village's secrets.
One possible plot could be that Amy Fleming starts having vivid flashbacks of a past trauma. These memories start to affect her daily life, and she has to find a way to deal with them. Maybe she seeks help from a friend or a professional.
Another possibility is that she is protective of her relationship with Sonic. Fanfic might introduce elements that she feels are inappropriate or could potentially damage the 'purity' of what she has with Sonic. It's like she wants to safeguard the special bond they share in the official narrative from being sullied by unapproved fan - created stories.
Perhaps the aura guardian was mind - controlled. An evil force took over its mind and made it act against Ash. In this case, the story could revolve around Ash trying to break the mind - control and save his friend. It would involve a lot of action and mystery as Ash figures out what's wrong and how to fix it.
One common plot could be that Amy Rose is kidnapped by a villain who wants to use her as bait to lure Sonic. The kidnapper might think that Sonic would come to save her, and they could set up a trap for him. Another plot could be that the kidnapper has a personal vendetta against Amy Rose herself, perhaps because she got in the way of their evil plans before. There could also be a plot where Amy Rose is kidnapped by mistake, and the kidnapper realizes their error but still decides to hold her captive for some other reason, like ransom or information.
In a 'amy lee my immortal fanfic', there could be a story set in a parallel universe where the song has magical powers. The main character, a big fan of Amy Lee, discovers that whenever they sing 'My Immortal', they can travel through time to moments in their past related to their own lost loves. This leads to a series of adventures where they try to correct the mistakes they made in those relationships, all while being guided by the spirit of Amy Lee that seems to be present in the song.
It could be a way to break away from the traditional narrative. Fanfics often experiment with different scenarios. By having Amy Rose die, the writer can take the story in a completely new direction, one that might not be possible in the original canon.