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.
In this fanfiction, a possible plot could involve the clone army being sent on a secret mission to a far - off land. There, they discover a lost ninja technique that could change the balance of power in the ninja world. However, they have to face many challenges, such as hostile locals and difficult terrains. The clones would need to work together and use their unique skills, which are based on Naruto's abilities, to succeed.