Perhaps the plot starts with Naruto's village facing a new and unknown threat that their traditional ninja skills can't handle. Monkey D. Dragon somehow arrives in the Naruto world and offers to train Naruto as he sees similarities between Naruto's struggle for peace and his own. During the training, Naruto discovers new ways of using his chakra and also learns valuable lessons about leadership and freedom from Dragon. This then helps him when he returns to his world to face the threat.
In this fanfiction's plot, it could be that Monkey D. Dragon has a prophecy about Naruto and his role in the grand scheme of things. So he travels to the Naruto universe to train Naruto. The training includes not only physical and combat skills but also mental and philosophical teachings. Naruto, in turn, uses this new knowledge and skills to unite the different ninja clans in his world in a way that was never thought possible before, creating a more harmonious and powerful ninja society.