The Naruto movies have never been in direct canon with the shows, and followed no particular story line. However, the NCU will tell the story of the Hidden Leaf Village and its star shinobi, Naruto. Here is my Contest Entry for the "Moviepilot Contest: Create The Next Cinematic Universe!"
The NCU (Naruto Cinematic Universe)
I. Hidden Leaf: Origins
The first movie of the NCU tells of the origins of the Hidden Leaf Village. It starts with the Warring States Period and the rivalry between the Senju and Uchiha tribes. After the battle between the soon-to-be First Hokage and Madara Uchiha, it switches to the first conflict between Shinobi, and ends with the death of the Second Hokage.
II. Adventures of the Sannin
The next movie will be the story of Jiraiya, Tsunade, and Orochimaru, better known as the Sannin. The movie will start out with their training under the Third Hokage, and move to their involvement in the Shinobi conflicts. Then, it will show their individual adventures before the events of present day.
There will be other movies involved in the NCU, such as Uzumaki Tales and the Uchiha Chronicles, the stories of Naruto and Sasuke, respectively. There would also be a movie which shows the events of the first Naruto series, then another Uzumaki Tales and Uchiha Chronicles. But the real climax of the story will be the two-parter:
III. War: Naruto v. Akatsuki
The two-parter will be about the conflict with the Akatsuki, with different events taking place, such as Sasuke vs. Itachi, Jiraiya vs. Pain, Sakura vs. Sasori, and many more. It will culminate into the destruction of the Akatsuki, and the battles leading up to it.
Well, let me know if you want the NCU to come to fruition, and have a great day!