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.
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.
First, think about the personalities of your human Ninja Turtles. Are they more like the original turtles in terms of their traits? Then, come up with a basic plot. It could be something simple like they are trying to stop a local crime wave.
Krang from Dimension X could also be a great villain. He might be interested in the human sister because she has some unique knowledge or ability that he wants to use for his own evil plans in taking over Earth. He could send his minions to capture her and the Turtles would have to journey to Dimension X to save her.
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.
Leonardo is often popular. In human fanfiction, he might be depicted as a strong and noble leader even in human form, guiding the other turtles and any human allies. He could be the one who tries to uphold justice in a human world.
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.
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.
April O'Neil is a classic choice. She's a human character who has a long - standing relationship with the turtles. Her skills as a reporter can add an interesting dynamic to the story.