Characters from Naruto and Ghost in the Shell can be combined in fanfiction in various ways. For example, the ninja's stealth and combat skills could be paired with the cybernetic enhancements of the Ghost in the Shell characters. Kakashi could get a cybernetic sharingan upgrade that combines the power of his original sharingan with the advanced technology. And the Ghost in the Shell characters could be given chakra - like energy sources, which would change the way they operate and fight. This would create new and exciting storylines and character developments.
The characters can be combined by having them team up. For example, Naruto and Luke Skywalker could join forces. Naruto's energy and determination along with Luke's connection to the Force would make a powerful duo. They could face common enemies like the Sith or rogue ninja. Another way is to have them teach each other. A Jedi could teach a ninja about the Force, and a ninja could teach a Jedi some ninja techniques.
Naruto could obviously be one of the main characters. He could interact with the Ghost in the Shell characters, like Major Kusanagi. Another could be Kakashi. His Sharingan and intelligence would make him a great character to explore the blend of Naruto and Ghost in the Shell concepts. Also, Batou from Ghost in the Shell could be a main character if the story focuses on the more technological and combat - heavy aspects of the crossover.
Sasuke could also be a main character in such a fanfiction. His thirst for power and his Sharingan could make him a key figure. He might be interested in the advanced technology in Ghost in the Shell as a way to further his own goals. And perhaps he would cross paths with some of the Section 9 agents.
They can be combined through a portal concept. A portal opens between the Naruto universe and the Transformers universe, bringing Naruto and Arcee together. Then they can work towards a common goal like saving both universes from a threat that spans across dimensions.
Another way is to put them in a completely new setting. Imagine Naruto and Azula in a modern - day city. Naruto would have to adapt his ninja skills to the urban environment, and Azula would have to hide her fire - bending. They could get involved in a mystery or a fight against an underground organization, and their different skills and personalities would play a big role in the story.
Freya could also be a spirit or a deity in the Naruto universe. Naruto, who has had experiences with powerful beings like the tailed beasts, could interact with her. She might bestow some special power or knowledge upon him, and their relationship could develop as Naruto tries to understand and use this new gift while also learning more about Freya's nature.
Well, they could be combined by having a magical portal that connects their two worlds. So Naruto could step through and meet Renesmee. Then they could go on adventures together, like exploring the forest around Renesmee's home or Naruto showing her his village.
In fanfiction, the combination could start with Sansa being intrigued by Naruto's strange appearance and abilities. She might ask him to teach her some of his skills. Naruto, being the kind - hearted person he is, agrees. As they train together, their relationship grows. Naruto could also introduce Sansa to the concept of different 'worlds' as he comes from a very different place. This could open up new storylines where Sansa tries to find a way to visit Naruto's world or they try to bring some of Naruto's world's positive elements to Westeros.
Perhaps Naruto is mistaken for a prophesied hero in the Jade Emperor's realm. So, he is given special treatment and tasks. But Naruto has to convince the Jade Emperor and others that he is from a different world and still wants to help. In the process, their characters interact and influence each other.
The sharingan from the Naruto universe might be able to analyze the patterns of Ikaruga's power usage. A character like Sasuke could then teach an Ikaruga character how to better control their powers based on the insights from the sharingan. In return, the Ikaruga character could show Sasuke how to use their polarity powers in a more strategic way in combat.