Maybe in this fanfiction, the virus in Z Nation is some kind of dark chakra - like thing. And the characters from Naruto have to use their chakra - related powers to find a cure. Sasuke could use his Sharingan to analyze the virus and see if there are any patterns or weaknesses.
One idea could be a crossover where Naruto characters end up in the Z Nation world. For example, Naruto with his shadow clone jutsu could be really useful against the zombies. He could send out clones to distract the zombies while the group tries to find a safe place.
A more complex fanfiction could involve a crossover of the two universes' viruses. The virus in Z Nation and the vampire virus in Twilight somehow interact. Bella, being in the middle of it, has to figure out how to stop a new, more dangerous threat that emerges from the combination of these two 'viruses'.
One idea could be a crossover where Goku and Naruto meet. Maybe they start off as rivals, each thinking their own world's way of fighting is superior. But then they face a common enemy that forces them to combine their powers. For example, a powerful demon that can absorb chakra and ki. They would have to learn from each other's techniques to defeat it.
One idea could be a story where the Navy is tasked with transporting survivors during the World War Z apocalypse. They have to deal with zombie attacks on their ships and at ports.
One idea could be a crossover where the powerful Saiyans from Dragon Ball Z end up in the Sekirei universe. They might get involved in the Sekirei Plan, either as protectors or accidental disruptors. For example, Goku could befriend some of the Sekirei due to his kind nature and his love for a good fight.
One idea could be that Danny, using his ghost powers, somehow gets transported to the Dragon Ball Z universe. He might initially be mistaken for an otherworldly being. He could team up with Goku and the gang, and use his intangibility and invisibility to help in battles against foes like Frieza or Cell. For example, he could sneak up on enemies and disrupt their energy blasts from within.
One idea could be a crossover where Goku meets Superman. They could have a friendly sparring match to test each other's strength. Maybe they start off misunderstanding each other's motives but then realize they are both protectors of their respective universes.
Perhaps in the fanfiction, North Korea has developed some sort of special technology or antidote that could potentially stop the spread of the zombie virus in the World War Z scenario. This would make them a key player in the global fight against the zombie apocalypse. They might share this technology with other countries in exchange for resources or alliances.
One idea could be to have characters from Naruto end up in the world of Danmachi. For example, Naruto himself could find his way into the dungeon and his ninja skills would be put to the test against the dungeon monsters. His shadow clone jutsu could be used in interesting ways, like sending clones into different dungeon levels to scout or fight. Another idea is to have the concept of chakra introduced into the Danmachi world. This could change the way adventurers fight and level up. Maybe some of the Naruto characters could train the Danmachi adventurers in new combat techniques.
One idea could be a crossover where Naruto is somehow transported to the Star Wars universe and meets Padme. Maybe he uses his ninja skills to protect her from the Sith.
Another concept is that Naruto is sent to Middle - earth. There, he could use his ninja skills and chakra powers. He and Gandalf could team up to fight Sauron. Naruto's ability to make friends and inspire others would be really useful in uniting the different races of Middle - earth against the common enemy.