One common theme is the struggle between loyalty and duty. The Shield Agent often has to balance their loyalty to their agency or organization with their newfound connections in the Naruto world. Another theme is the exploration of hidden powers. Since they are agents, they might have some special abilities that they discover while in the Naruto universe.
One possible plot could be that Naruto is forced to become the shield due to a prophecy. He has always been a protector, but this time it's on a whole new level. The fanfiction might explore his internal struggle as he accepts this new role. He may have to face the fact that he will be permanently changed into a shield, but he does it anyway to safeguard the future of the ninja world. His friends might try to find a way to reverse it, but Naruto is resolute in his decision to be the shield for as long as needed.
Steve Rogers could be a great ally. Steve's strong sense of justice and leadership would mesh well with Naruto's own values. They both have a history of standing up against powerful enemies. Steve could also learn a lot from Naruto's unique fighting style and his ability to never give up. For example, Naruto's use of chakra to enhance his physical abilities might inspire Steve in new ways of combat.
One interesting crossover could be the S.H.I.E.L.D. agents trying to understand and work with the ninja world of Naruto. For example, Coulson might be intrigued by the unique abilities of ninjas like Naruto's shadow clones. He could see potential in using some of their techniques for S.H.I.E.L.D. operations. Another aspect could be S.H.I.E.L.D. agents trying to adapt to the chakra system. Maybe Fitz - Simmons could study it and come up with some wild theories about how it relates to the science they know.
It could be a new, powerful ninja from a far - off land who wants to destroy Konoha. This ninja might have a grudge against Naruto specifically and forces him to become the shield to protect the village.
One possible plot could be Naruto being sent to the Marvel universe through some kind of interdimensional rift. He joins S.H.I.E.L.D. and uses his ninja skills to help in their missions. For example, his speed and stealth could be very useful in espionage operations. He might also teach some of the agents his unique jutsu, like the Shadow Clone Jutsu, which could be used for various strategic purposes in battles against super - villains.
Well, the characters' abilities could combine in some unique ways. The ninjas from Naruto have their own form of teleportation like the Body Flicker Technique. S.H.I.E.L.D. could try to understand and replicate this for their own use. Inversely, S.H.I.E.L.D. has advanced weaponry. Imagine Naruto using a S.H.I.E.L.D. - made energy weapon along with his ninjutsu. It would be a powerful combination that could take on some of the toughest enemies in both the Naruto and Agents of Shield universes.
One great Naruto Shield Agent fanfiction is 'The Hidden Agent'. It has an interesting plot where the main character, an agent in the Naruto universe, has to face various challenges while keeping his true identity a secret. The story is full of action and mystery.
One interesting crossover could be the characters from Naruto learning about the unique shield abilities in Rising of the Shield Hero. For example, Naruto might be intrigued by Naofumi's shield and how it can transform and be used in different ways. Another aspect could be the ninjas from Naruto teaching the heroes in Shield Hero some of their combat techniques.
First, you need to be familiar with both Naruto and Shield Hero universes. Know the characters, their powers, and the rules of their worlds. Then, come up with an interesting plot. It could be a crossover where characters from both series meet and have to overcome a common threat.