Character development is key. If you're bringing Naruto characters into the Cloak and Dagger world, show how they adapt. Naruto, for instance, is a very positive and determined character. How would he react to the often - darker situations in Cloak and Dagger? Also, make sure the dialogue is in - character. The language used by the Cloak and Dagger characters is different from that in Naruto. Blend it well so it feels natural. And don't forget to add some action scenes that showcase the powers of both universes.
First, you need to do your research on both Naruto and Cloak and Dagger. Know the characters, their powers, and the settings well. For example, in Naruto, the different clans and their jutsus are important elements. In Cloak and Dagger, the light and dark powers and the social issues in their world matter. Then, come up with a unique plot. Don't just copy existing storylines. You could start with a situation like a dimensional rift that brings the two worlds together.