A neighboring Daimyo who is jealous of the prosperity of the Daimyo our guard is protecting. He hires a group of powerful and merciless ninjas to eliminate the Daimyo so that he can take over the land. This would make the conflict not only about protecting the Daimyo but also about preventing a war between the two lands.
It could be a rogue ninja who was once part of the Daimyo's own forces but turned against him for some reason, like not getting the recognition he thought he deserved. He now wants to take revenge by assassinating the Daimyo.
Perhaps an ancient evil spirit that has been awakened due to some dark magic rituals performed near the Daimyo's palace. The spirit targets the Daimyo because his positive energy and influence over the land is a threat to the spirit's plans of spreading chaos. The Daimyo guard would then have to figure out how to combat a supernatural foe, which is different from his usual ninja opponents.
One possible plot could be that the Daimyo guard has to protect the Daimyo from a secret ninja clan that has a vendetta against him. The guard uses his unique skills, perhaps some special jutsu passed down in his family, to fend off the attackers.
Naruto would be a likely main character. Since he is the hero of the Naruto series, he could be involved in any story related to the Fire Daimyo. His friends like Sasuke or Sakura could also be part of it. They might be sent on a mission by the Hidden Leaf to protect or assist the Fire Daimyo.
There could be a group of rogue ninjas within the Sound village itself. These ninjas oppose the Daimyo's new policies and reforms. They want to keep the old ways, which were more about power - grabbing and using dark jutsu. So they start causing chaos within the village, trying to undermine the Daimyo's authority.
A powerful female character can also be a main character in 'naruto daimyo fanfiction'. She could be a diplomat who tries to negotiate between the daimyo and the ninja villages. Her charm, intelligence, and political acumen make her a central figure in the story.
Temari could also be a potential character. Given her status in the Sand Village and her strong - willed nature, she would bring a different dynamic to the harem. There could also be some original characters created specifically for the fanfiction to add more variety.
Naruto himself could be one of the main characters. He has a strong sense of justice and loyalty, which would make him a great addition to an honor guard. His ability to inspire others would also be an asset.
It could be Orochimaru. He's always interested in new forms of power and experimentation. He might see Wolverine as an interesting specimen to study and try to extract his healing factor or adamantium for his own purposes. This would put him in direct conflict with both Wolverine and Naruto, who would naturally oppose Orochimaru's evil plans.
Danzo could be a great main villain in a Naruto Frankenstein fanfiction. He's always been power - hungry and secretive. He might use the concept of creating a Frankenstein - like being to gain more power for Konoha in his own twisted way, but really it's all about his own control. He could be using parts of dead ninja's abilities or something like that, and Naruto would have to stop him.
Orochimaru could be a likely main villain. He has always been interested in Naruto's power and body. Maybe he finally devises a plan to kidnap Naruto and use his body for his own reincarnation experiments.
It could be Orochimaru. He might be interested in stealing the exosuit to enhance his own powers and immortality research. He could see the exosuit as a new way to achieve physical enhancements beyond what his current jutsu can do.