One idea could be that the Ninja from Ninjago are transported to the TMNT's world. They team up to fight a common enemy like the Shredder who has somehow got hold of some dark magic from Ninjago. The Ninja can show the Turtles their unique fighting styles and the Turtles can introduce the Ninja to the sewers of New York as a base.
One common theme is power combination. When characters from different universes meet in the crossover, their powers often combine in unexpected ways. For example, in a Ninjago and Avatar: The Last Airbender crossover, the ninjas' elemental powers might interact with the bending abilities of the Avatar characters.
The plot could involve a new threat emerging that affects both worlds. This threat could be a powerful sorcerer who wants to combine the technology of the TMNT world with the magic of Ninjago. The Ninja and the Turtles would have to put aside their differences and work together. They would travel between the two worlds, exploring each other's unique environments like the Ninjago Monastery and the TMNT Lair.
Another good one is 'Ninjago and DC Comics Crossover'. Here, the ninjas from Ninjago get involved with the heroes and villains of the DC universe. Imagine the Green Ninja facing off against Superman or the villains of Ninjago teaming up with the Joker. It makes for some very unique and engaging storylines.
One idea could be that the ninjas from Ninjago end up in the world of Slugterra by some magical portal. They then have to learn about slug slinging and team up with the local sluggers to fight a common enemy. Maybe an ancient evil that threatens both their worlds.
One possible plot could be that the ninjas from Ninjago accidentally stumble into the world of Chima while on a mission through a magical portal. They find that the animal tribes in Chima are facing a new threat that they can't handle on their own. The ninjas decide to help, using their unique skills. For example, Kai could use his fire powers to combat an ice - based enemy that the Chima tribes are struggling with. Meanwhile, the Chima characters could introduce the ninjas to their own ways of fighting, like using their vehicles and the power of Chi. This would lead to an exchange of fighting styles and strategies, and in the end, they would defeat the common enemy together and the ninjas would find their way back home.
Naruto's ability to use chakra and his shadow clone jutsu could be combined with the Ninjago ninjas' elemental powers. For example, Naruto could create shadow clones to help Kai with his fire - based attacks in a battle.
Imagine if there was a tournament that brought the best fighters from both universes together. Naruto, Sasuke, and the others from the Naruto world, and Kai, Jay, and the rest from Ninjago. They start off competing against each other but then realize there is a greater threat lurking. A group of shadowy figures wants to steal the powers of both ninjas and warriors. So, they must put aside their differences and combine their skills to fight this new enemy.
A possible plot for this crossover fanfiction is that the worlds of Ninjago and Chima start to merge due to some magical mishap. This causes chaos as the different species and cultures collide. The heroes then have to figure out how to separate the worlds again. For example, the ninja from Ninjago might have to work with the lions from Chima. Another idea is that a group of villains from both worlds team up and the heroes have to form an alliance of their own. They would need to overcome their differences and learn from each other's fighting styles. There could also be a story where a Ninjago character is transported to Chima and discovers a long - lost relative from there, which adds a personal touch to the adventure.
I liked the one where Lego Ninjago crossed over with 'Ben 10'. In this fanfiction, the ninjas had to work with Ben to stop an alien invasion that was also affecting Ninjago. The author did a great job of mixing the two universes' lore and making it seem like a natural combination. Ben's ability to transform into different aliens added a lot of variety to the story.