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.
One idea could be a fanfiction where the spots of the dalmatians have magical powers. For example, they can create portals to different places. Another could be a story about a dalmatian puppy who is born without spots and his journey to find a way to get them. Maybe there could also be a fanfiction where the spots are actually a map leading to a hidden treasure.
The opportunity for alternate universes. Fanfiction writers can create their own versions of what could have happened in the Mystery Spot. Maybe in one fanfic, Sam figures out a way to break the time loop much earlier. Or perhaps there are different supernatural creatures involved. It allows for a lot of creativity and gives fans a new take on a beloved episode.
You can start by looking on fanfiction websites like Archive of Our Own (AO3) or FanFiction.net. These platforms have a wide range of Supernatural fanfictions, including those centered around the Mystery Spot. Just use the search function and type in 'Supernatural Mystery Spot' to get relevant results.
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.
Start by researching the Mystery Spot itself. Find out what makes it mysterious in real life. Then, think about the type of supernatural elements you want to include, like vampires, werewolves or magic. After that, create your main character who will be drawn to the Mystery Spot for some reason.