One interesting plot idea could be an alternate universe where the turtles have different elemental powers. For example, Leo could control ice, Raph fire, Donnie electricity and Mikey wind. This would change their fighting styles and how they interact with villains.
A story where the turtles meet their future selves. Their future selves could come back in time to warn them about a great danger that they have to face together. This would involve a lot of self - reflection for the present - day turtles as they see how they might turn out in the future and also have to work with their more experienced counterparts to save the day.
A plot where the turtles swap personalities. So the usually serious Leo becomes the goofy one, Raph is the tech - savvy one like Donnie, Donnie turns into the hot - headed one like Raph, and Mikey becomes the overly cautious leader. It would lead to a lot of comical and also character - developing situations.
One idea could be an OC who is a new mutant in the city. They could have a unique power like the ability to control plants. At first, they are scared and confused about their new form and powers, but as the story progresses, they learn to use it for good and join the turtles in their fight against the bad guys.
One idea could be that the Turtles from 1987 end up in the 2003 universe and have to adapt to the darker and more serious tone. They could team up with the 2003 Turtles to fight a common enemy like the Shredder. The 1987 Turtles' more light - hearted and comical ways might initially clash with the 2003 Turtles' brooding nature, but they eventually learn from each other.
A possible plot is that an ancient evil that was sealed away in the 2003 universe is accidentally awakened by the arrival of the 2012 turtles. The 2003 turtles initially blame the 2012 ones but then realize they need to work together. They combine their strengths, with the 2012 turtles' modern thinking and the 2003 turtles' deep knowledge of ancient ninja lore, to defeat the evil.
One idea could be that the Turtles from 2003 get transported to the 2012 universe and they have to deal with the different versions of their enemies. For example, the Shredder in the 2012 version might have some new powers or tactics that the 2003 Turtles aren't used to.
Perhaps the mutagen that created the Turtles has some strange reaction when exposed to the Dragon Balls' energy. This could lead to new powers for the Turtles and a whole adventure about controlling and understanding these powers while also dealing with the Dragon Ball Z characters' reactions to them. For example, Vegeta might be initially suspicious and see the Turtles as a threat to his power status.
Perhaps a plot where Leo discovers some new powers or abilities that are related to his pregnancy. It could be something that he has to learn to control quickly. And then there could be a story arc about the team finding a way to ensure a safe delivery for Leo, which might involve seeking out some very rare or magical items.
One idea could be a Winged OC who is from a different dimension and has the power to heal. The OC could encounter the TMNT during a battle where one of them is seriously injured. Another plot could be that the Winged OC is on a quest to find a lost artifact, and the TMNT get involved either by accident or because they also have an interest in the artifact. Or perhaps the Winged OC is a runaway from an evil organization that the TMNT are trying to take down, and they form an alliance.
One idea could be that the Turtles end up in the Underground world of Undertale. They might have to navigate through the various regions, like Snowdin or Hotland, using their ninja skills. For example, they could use their stealth to avoid some of the more dangerous monsters. Another plot could involve the characters from Undertale being brought to the Turtles' New York. They would then have to deal with the Foot Clan and other threats in this new, strange environment.
One idea could be that as a girl, Leo has to face different challenges in leading the team. Maybe she has to deal with more doubts from others at first because she's female. But she overcomes them with her skills and determination.
A snake OC fanfiction could focus on a snake that was experimented on by the Kraang. It gains super - intelligent and psychic powers. The Turtles initially see it as a threat but then realize it just wants to find a place in the world. They help it control its powers and it becomes an ally. It could have a really cool design with purple and green scales from the Kraang experiments.