One idea could be that the clone commandos are sent on a special mission to infiltrate an enemy base. They use their unique Naruto - style skills like shadow clones to create diversions and gather intelligence.
Another plot could involve the clone commandos being created specifically to deal with a threat that the regular ninja forces can't handle. They start out as just following orders but gradually develop their own personalities and relationships. They might face a moral dilemma when they realize that their existence as clones might be considered expendable by some in the ninja hierarchy, leading to a story about their struggle for recognition and self - worth.
Obviously, the clone commandos themselves could be the main characters. Each clone could have different abilities or characteristics that set them apart.
In this fanfiction, perhaps Naruto as a Darkseid clone discovers new powers. Since Darkseid is a powerful being in the DC universe, Naruto could inherit some of that raw power. He might have to learn to control it, just like he learned to control his chakra. His friends in the Naruto world could be either afraid of him or try to help him come to terms with this new identity.
One possibility could be that Naruto somehow gains Superman - like powers. Maybe through some strange scientific experiment or a magical encounter. He could then use his newfound abilities, like super strength and flight, in combination with his ninja skills. For example, he might use super speed to perform his shadow clone jutsu even faster, overwhelming his enemies in a way that was not possible before.
One common theme is adaptation. The clone commandos have to adapt to new environments, whether it's a different time period, a different planet, or a different genre of setting.
One idea could be that the clone develops its own unique personality over time and forms a special bond with Naruto that is different from his relationship with others. It could start to have dreams and desires separate from its original purpose as a clone.
A plot could revolve around the clones being sent on a special mission. Since they are clones, they might not have all the emotional baggage of the originals. They could approach the mission with a fresh perspective and use their combined skills in new and unexpected ways. Maybe they have to infiltrate an enemy base, and their ability to think like Naruto and Naruko but also act independently gives them an edge.
A plot could involve the crow clones being used by an enemy to spy on Naruto and his friends. However, the clones gradually develop a sense of loyalty towards Naruto and his cause, and they end up double - crossing the enemy. This could lead to a great battle where the clones prove their worth and become an integral part of Naruto's team.
Maybe Naruto uses his clone training not just for physical skills but also for mental and strategic training. He could create clones to play shogi or solve complex puzzles against each other. This would enhance his thinking skills and help him in battles where strategy is crucial. The clones could then share their insights with the original Naruto.
Maybe in the fanfiction, the clones start to gain special powers different from Naruto. For example, some clones could have the ability to control time on a small scale. This would create a whole new dynamic in the battles and the overall story.
One idea could be the clones developing their own personalities over time. Since they are all part of Naruto, they might start to have different outlooks on life. Another could be using the clone army to fight a new and powerful enemy that the regular shinobi forces can't handle alone.