Perhaps Atem turns evil due to a grudge from his past life that resurfaces. He discovers some hidden truth about his death or the people around him back then. Feeling betrayed, his sense of justice twists into a desire for revenge. He starts to target those he believes were involved in the wrongdoings against him, using his powerful dueling skills in a more menacing way.
One possible plot could be that Atem is influenced by a dark magic artifact. Maybe he stumbles upon an ancient relic during an excavation in the afterlife. The relic starts to corrupt his thoughts, making him believe that only through domination can there be true order in the world. So he begins to use his powers to subdue the spirits around him.
The Spirit of the Millennium Items could also be the main antagonist. They were initially in harmony with Atem, but with his turn to evil, they might try to resist his control. Since they are powerful entities in their own right, they could become a force against Atem. They would not want to be used for evil purposes and would fight back against Atem's newfound malevolence.
Well, one possible plot could be that the girl is betrayed by her friends, and this leads her to become evil as she decides to take revenge on them. For example, she might start spreading false rumors about them or sabotaging their relationships.
Perhaps Marco is injured while trying to protect Star from an assassin sent by one of the villains in the series. This could lead to a story where Star blames herself for his injury and has to overcome her guilt while also taking care of Marco and finding a way to stop the assassin from coming back for another attempt.
One possible plot could be that Tails is exposed to some dark energy or a powerful, corrupting artifact. This makes him gradually turn against his friends. He might start using his intelligence to outwit Sonic and the others for his new, evil goals.
Well, one possible interesting plot could be the exploration of a darker Naruto who has been pushed to the edge by neglect. Maybe he forms unexpected alliances with characters usually considered antagonists in the original story, like Orochimaru, but for different motives than in the canon. He might be seeking power not just for himself, but to expose the flaws in the ninja system that led to his neglect.
One possible plot is that the evil robot monkey is created by a mad scientist for world domination. It uses its robotic abilities to steal important data and technology to further its master's evil plans.
One interesting plot could be Atem and Yugi exploring ancient Egyptian mysteries together in the modern world. They might use Atem's knowledge from his time as a pharaoh and Yugi's skills with the Millennium Puzzle.
In some 'peter doesn't turn to dust fanfiction', the plot might revolve around a character coming to Peter's rescue at the last moment. This could be a character with unique powers or knowledge. They could use their abilities to reverse the process that would make Peter turn to dust. Or perhaps there's a magical or technological device that is introduced in the story that stops Peter from turning to dust. The fanfiction could then explore how Peter and the other characters deal with this new situation and what new challenges or opportunities it presents.
One possible plot could be that the murderer is a jealous rival. Maybe this rival has always been envious of Percy's popularity or special abilities, and finally decides to get rid of him. Another plot could involve a mystery where Percy is murdered and his friends have to piece together the clues to find out who did it. It could be that the real killer is someone they least expected, like a seemingly friendly acquaintance who has a hidden agenda.
One possible plot could be that Alderheart succumbs to an illness that has been plaguing the Clan. His friends and family are left to mourn his loss and deal with the void he leaves behind in the Clan's medicine den.