One idea could be to have a character from Naruto end up in the Cloak and Dagger universe. For example, Naruto himself could be transported there and his unique abilities like the Rasengan would be a shock to the characters in that world. He might team up with Cloak and Dagger to fight against a common enemy, perhaps a group that is trying to steal 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.
Kabuto could also be a great antagonist. After learning so much from Orochimaru, he could see the potential in the cloak and dagger and want to use them to prove himself as a powerful ninja. He could be constantly trying to outwit Naruto and take the items for himself.
Maybe there's a plot where the cloak and dagger are not just physical objects but hold some sort of ancient ninja magic. Naruto discovers that the cloak can make him invisible in certain conditions and the dagger can cut through any kind of barrier. He has to figure out how to master this magic to save the village from a new threat.
One popular idea is exploring the backstories of Cloak and Dagger in more depth. Maybe how they got their powers in a different way than in the original. Another could be a 'what if' scenario where they are in a different city dealing with different villains. And also, fanfics often explore their relationship, like a time when they had a big fight and how they reconciled.
It could be a rogue ninja who has a vendetta against Naruto. This ninja might have a similar cloak with dark powers and a dagger that has some sort of curse on it. He wants to prove himself stronger than Naruto by stealing Naruto's cloak and dagger and using them for evil.
Overall, Cloak and Dagger stays somewhat true to the comics. Some characters and plotlines are adapted, while others are changed for better storytelling in the TV format. There are additions and omissions, but the core essence remains.