One idea could be that Ceez is a new recruit in a ninja clan led by Ninja. Ceez has some unique powers that the clan has never seen before, like the ability to communicate with animals. This causes some jealousy among the other ninjas at first but eventually helps the clan in a big battle against an evil sorcerer.
A powerful warlord who wants to conquer both Ceez's world and the ninja world. He has an army of dark warriors and uses dark magic to try and achieve his goals. He sees Ceez and Ninja as the biggest threats to his plans, so he constantly tries to eliminate them.
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.
Maybe a fanfic where all the characters are transported to a modern-day world. Naruto would have to adapt to things like technology while still trying to use his ninja skills. He could end up using his shadow clones to do multiple jobs at once to earn money and also keep his ninja training going.
One idea could be an ice ninja from a hidden village in the far north coming to Konoha for a ninja exchange program. They could introduce unique ice-based jutsus to Naruto and his friends, like creating ice clones that are more durable than regular shadow clones. Another plot could involve an ice ninja villain who is trying to freeze the world and Naruto has to learn a new fire - ice combined jutsu to stop them.
One idea could be a medical ninja who discovers a new healing technique that has side effects that no one expected. This could lead to a race against time to find a cure while also dealing with the political implications within the ninja villages.
One idea could be a group of pokemon ninja trainers who have to protect a rare and powerful pokemon from an evil organization. The trainers could use their ninja skills, like stealth and quick attacks, along with their pokemon's abilities to outwit the villains.
Perhaps in this 'Naruto New Game Plus Fanfic', the world itself is changed in the new game plus. There are new areas to explore, like a hidden underground ninja village that was previously inaccessible. Naruto and his friends set out to discover this new place, uncovering secrets about the ninja world's past along the way, and also facing new threats that lurk in these uncharted regions.
You could write a fanfic where the Teenage Mutant Ninja Turtles discover a hidden underground city beneath New York. In this city, there are mutants with different abilities and cultures. The turtles have to learn to navigate this new society while also facing a threat that wants to use the underground city's resources for evil. Or, a fanfic that focuses on the turtles' training. What if they had a new mentor who taught them a completely different style of martial arts? It would change the way they fight and interact with their enemies. Also, a story about the turtles getting shrunk to a tiny size and having to survive in a world that's now giant to them could be really interesting.
Maybe in the fanfic, there is a special mission where Naruto and the Ninja Gaiden characters need to retrieve a powerful and ancient artifact. The Ninja Gaiden side has their own reasons for wanting it, like protecting their village or clan, and Naruto is involved because it has something to do with the balance of his world too. They start off not trusting each other but as the adventure progresses, they form a strong bond.
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.