Perhaps a new character could be introduced as the main antagonist. A rogue ninja from a far - off land who has heard rumors of the powerful cloak and dagger in the Hidden Leaf Village. This ninja has his own motives, like using the items to take over all the ninja villages, and sees Naruto as the only obstacle in his way.
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.
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.
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.
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.
The main characters in the 'Cloak and Dagger Graphic Novel' are Cloak and Dagger. Cloak is a rather mysterious figure. His power is tied to his cloak, which allows him to perform feats such as disappearing into the shadows and emerging in other locations. Dagger, in contrast, has a more positive - energy - based power. She can create daggers made of light. Their powers are complementary, and they are the central focus of the story. They face different challenges together and their relationship, whether it's a friendship or something more complex, is an important aspect of the graphic novel.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.