Perhaps a fanfiction where the human Ninja Turtles travel back in time to the era when the original turtles were created. They could interact with the mutagen that made the turtles what they are and maybe change the course of their own existence in some way. For example, they could try to prevent certain villains from ever being created.
One idea could be a human character who discovers the Ninja Turtles' lair by accident and has to prove they can be trusted. Maybe they help the turtles in a battle against a new enemy, like a mutated creature from the sewers that the turtles hadn't faced before.
Maybe the human sister is a scientist who is working on a project that could potentially help the Ninja Turtles in their fight against evil. But the bad guys find out about it and try to stop her. Or she could be an artist who uses her art to inspire the Turtles and give them new ideas for their strategies. She might also have a secret past that is somehow connected to the mutagen that created the Turtles.
One idea could be a story where the turtles become human for a day and have to navigate high school. They'd struggle with normal teenage things like fitting in and dealing with bullies, all while trying to hide their turtle identities.
A really cool idea for ninja turtles fanfiction would be to have a story set in a post - apocalyptic New York. The Turtles would have to deal with new threats that emerged after the world as they knew it was destroyed. They might have to face mutated versions of ordinary animals and humans that are far more dangerous. There could also be a sub - plot about the Turtles trying to find other survivors and rebuild some sort of community. This would give a chance to explore their leadership skills and how they adapt to a completely different environment.
One idea could be a story where the turtles have to blend in as humans in a high school setting. They could struggle with normal teenage things like exams and dating while also hiding their turtle identities.
A crossover with the X - Men could also be cool. Picture the Turtles in the mutant - filled world of the X - Men. They might have to deal with the complex politics of mutants while also facing off against villains like Magneto. The Turtles could learn from the X - Men's experience in dealing with a world that fears and hates mutants, and vice versa.
A realistic integration could happen through family ties. Imagine a human character is related to someone who was involved in the accident that created the mutagen. This connection could lead them to the turtles, and they could work together to either reverse the mutagen's effects or use it for good in some way. It also adds an emotional layer to the story as the human has a personal stake in the turtles' world.
Another possibility is a crossover with the Ghostbusters. The Turtles and the Ghostbusters could join forces in New York City. The Turtles' knowledge of the sewers and the Ghostbusters' ghost - busting equipment would be a great combination to deal with some spooky paranormal activity in the city.
One idea could be a story where the Teenage Mutant Ninja Turtles discover a hidden mecha technology in the sewers. They have to figure out how to use it to defeat a new, powerful enemy. Maybe it gives them new abilities like enhanced speed or the power to fly.
One idea could be exploring the turtles' origin in more depth from a different perspective. Maybe a new character discovers a hidden aspect of their mutation process.