Begin by brainstorming the key elements of both Naruto and the other crossover universe. Let's say it's a Naruto and Dragon Ball Z crossover. Think about how Naruto's chakra system would interact with the ki in Dragon Ball Z. Consider the power levels and how they would compare. You also need to establish the setting. Will the story take place mostly in the Naruto world, the Dragon Ball Z world, or a new hybrid world? After that, start plotting out a basic story arc, like an evil force from one world threatening the other and how the characters from both will team up to stop it.