A fanfiction could be about a character who discovers that skipping stones was an ancient art lost in the Supernatural world. As they start to learn and practice it, they unearth secrets about their own past and the history of the hunters.
The main themes in Supernatural often include family and sacrifice. In a skipping stones fanfiction, the act of skipping stones could be a family tradition among hunters. When a character skips stones, it could be a way to remember a lost family member, thus tying into the family theme. And if a character has to sacrifice their chance to skip stones (maybe it has some power - granting properties) to save another, it would incorporate sacrifice.
Perhaps a fanfiction where a character from The Raid has some sort of special ability like the characters in Supernatural. Maybe he can see ghosts or has some sort of psychic power. This new ability could help him during the Raid and also change his relationship with his team members. He might be seen as an outcast at first but later prove to be very valuable.
One idea could be exploring the backstories of the different bloodlines in more detail. For example, you could focus on a particular family within a bloodline and how they've been affected by the supernatural elements over generations. Another idea is to create a new character who is a hybrid of two different bloodlines and show their struggle to fit in or their unique powers.
One idea could be a crossover where Goku from DBZ ends up in the Supernatural universe and has to team up with the Winchester brothers to fight demons. He could use his ki blasts against the hordes of hell.
Maybe a fanfiction where a bagel shop in the Supernatural universe is a front for a secret society of hunters. The bagels there are made with ingredients that can ward off demons, and the story could revolve around the main characters uncovering this mystery.
One idea could be a character suddenly gaining supernatural powers and having to learn to control them while also dealing with the regular Supernatural threats. For example, a hunter who gets the power to see the future and has to figure out how to use it to prevent disasters in the hunting world.
One idea could be exploring the relationship between the characters in more depth. For example, focusing on how Sam and Dean's bond was tested during that episode. Another idea is to create an alternate ending where things took a different turn.
One plot idea could be Ketch getting involved in a time - travel adventure within the Supernatural universe. He could go back in time and interact with the Winchester brothers at different points in their lives, changing the course of events in unexpected ways.
A possible plot could involve the mystery spot being a place where the boundaries between the living and the dead are thin. A young girl, who has the ability to see ghosts, goes there to try and communicate with her deceased mother. But she soon realizes that there are malevolent spirits there too and she has to use her supernatural gift to protect herself and others who are drawn to the mystery spot's strange energy.
Well, you could have a fanfiction where a new character creates a chat room specifically for Supernatural characters to interact with each other outside of their usual battles. It could be a place where they share their fears and hopes. Maybe Castiel accidentally enters this chat room not knowing what it is and has some really funny exchanges with the other characters. Also, the chat room could be a time - traveling one where characters from different eras of the Supernatural universe can communicate.