Maybe a new character could be created specifically for this crossover. This character could be a hybrid of a familiar from 'familier of zero' and a werewolf. They would be an outcast in both worlds and the story could follow their journey to find acceptance and belonging in either world.
A werewolf alpha could be the main character. He enters the 'familier of zero' world and has to navigate the complex magic and politics there. His werewolf instincts could either help or hinder him as he tries to understand this new world and find a way back home.
A plot could involve a werewolf being sent to the 'familier of zero' universe. The werewolf's abilities would be a mystery and source of both fear and fascination. They could end up being hunted or befriended depending on how the story unfolds. It could also lead to a discovery of a common enemy between the two universes.
It could be a new ninja who has a special ability to sense the Zero Tails. This ninja might be an outcast in their village because of this strange ability, but it turns out to be the key to dealing with the Zero Tails.
Mega Man Zero could also be the main character if the story focuses on his adventure in the Naruto world. He would be the outsider, having to learn about chakra, ninja clans, and the political structure of the Naruto world. His combat skills and sense of justice would play a big role in how he navigates this new and strange world.
It could be a new vampire character that is created specifically for this crossover. This vampire could be a hybrid of some sort, half - vampire and half - something else, and their unique nature draws the attention of both the vampire world and the characters from 'The Originals'.
Perhaps an anti - hero could be the main character. They find the Infinity Armor and initially use it for their own self - serving purposes. But as the story progresses, they start to see the bigger picture and become more heroic, using the armor to protect not just themselves but also the different worlds they encounter during the crossover.
It could be a journalist. They are always looking for a big story, and stumbling upon the werewolf world gives them the ultimate scoop. But as they get closer to the truth, they start to transform into a werewolf themselves, which makes the story more complex and interesting.
Theodore could also be the main character. He's the kind - hearted and a bit more timid one. If he were the main character in a werewolf fanfic, it could be about how he overcomes his fear of the werewolf. Maybe he has a special connection with the werewolf, like he realizes that the werewolf is not all bad and tries to befriend it, which would be a very different take compared to the others.
Zero himself could be the main character in a sense. Imagine he somehow gets transported to the Naruto universe. He'd be a fish out of water at first, but his combat skills and sense of justice would make him a force to be reckoned with. He could start to learn about chakra and ninjutsu, and use his knowledge from his own world to help or even lead the Naruto characters in battles against new threats.
Another option is that a new character introduced in the crossover could be the main character. For instance, in a Naruto - Fullmetal Alchemist crossover, an alchemist from the FMA world could stumble upon Naruto's sealed state and make it their mission to free him, while also getting involved in the politics and power struggles of the Naruto world.
It could also be a new character created specifically for the fanfiction. This character could be from the world of the crossover and have some special ability or knowledge that helps in the fight against the Heartless. Maybe they have a deep understanding of the magic or technology in their world that can be used to counter the Heartless threat.