A plot could revolve around a mystery in the dark. For example, strange disappearances are happening only at night in the shadows. The protagonist has to figure out what's causing it, whether it's a supernatural being or a secret organization using the cover of darkness.
One idea could be a character discovering a hidden power within the shadows that they must learn to control. Maybe they are initially afraid of it but then realize it can be used for good.
Perhaps the fanfiction could focus on a group of friends who get lost in a shadowy, enchanted forest. As they try to find their way out, they encounter various challenges and strange creatures that lurk in the shadows, and they must rely on each other to survive.
For Shadow of the Colossus fanfiction, you could write about a hidden society within the Forbidden Land. They worship the colossi in a different way than the main narrative implies. Wander stumbles upon this society during his journey. Or, you could do a fanfic where the colossi are not actually the 'bad guys'. They are guardians of something far more important and Wander is being used by the shadowy forces that sent him on this quest. And finally, a story about how the magic or energy that powers the colossi affects the wildlife in the Forbidden Land in ways not shown in the game. For instance, there could be mutated or super - intelligent animals due to this energy.
Another plot idea is to create an alternate timeline within the 'a walking shadow' world. This could involve different events happening to the characters, leading to new relationships and challenges. For example, a character who was once an enemy could become an ally in this new timeline.
Perhaps they are living in a parallel universe where everything is dark and gloomy. Dark Naruto and Dark Kushina could be trying to find a way to break through to the normal universe. They might encounter strange versions of their friends and foes, and have to battle their own inner demons along the way. For example, Dark Naruto might struggle with the darker aspects of the Nine - Tails' power that he has fully embraced in this universe.
One idea could be exploring Dark Seraphina's origin. Maybe she was once a normal angel but something tragic happened that turned her dark. Another could be a story where she teams up with an unlikely ally, like a human with special powers, to fight a common enemy. It could also be interesting to write about her trying to redeem herself.
One idea could be exploring the backstories of the minor characters in more detail. For example, the life of a downworlder who has interacted with the main characters but whose story is not fully told in the original. Another could be a 'what if' scenario, like what if a certain character made a different choice during a crucial moment in the story. This could lead to a completely different chain of events and relationships.
One idea could be exploring how the prophecies are misinterpreted at first. Maybe the characters think it means one thing, but as the story unfolds, they realize it's something completely different.
Another plot idea could be a 'what if' scenario. For example, what if a certain event in Dark Harmony had a different outcome? This could lead to a completely different story line with new relationships and challenges for the characters.
Perhaps a story where a secret society meets only in the dark of night. The main character stumbles upon their meeting and gets drawn into a world of secrets, power struggles, and ancient rites.
A plot could involve a group of dark digimon forming an alliance to take over a particular area of the digital world. They start by targeting the weakest digimon settlements. The story could follow a young digimon trainer who tries to gather allies to fight back against this dark alliance. There could be many challenges along the way, like finding rare and powerful digimon to join the cause, and also dealing with the psychological warfare that the dark digimon use. For example, they might spread false rumors to cause distrust among the good digimon.
Perhaps a fanfiction could focus on the backstory of Harvey Dent before he became Two - Face. It could show his early days as a prosecutor and how his idealism gradually got corrupted, which would add more depth to his character in the Dark Knight universe.