A more complex fanfiction could involve a time - travel plot. Naruto travels to the future and meets Zero Two. He has to use his ninja knowledge and values to navigate the strange future world and help Zero Two in her battles against powerful foes. At the same time, he also tries to find a way back to his own time.
Another fanfiction concept could be a story where Zero Two somehow gets transported to the Naruto universe. She could be initially confused but quickly adapt and start learning ninja techniques. Maybe she forms a special bond with Naruto as they both have a sense of being different from others in their respective worlds.
One idea could be a crossover where Naruto and his friends end up in the world of Zero Two. They could team up with Zero Two and her squad to fight a common enemy that threatens both their worlds. Naruto's unique jutsu and leadership skills would blend well with Zero Two's combat abilities.
One idea could be that Naruto is somehow transported to the world of Horizon Zero Dawn. He could use his ninja skills to help Aloy in her battles against the machines. Maybe his shadow clone jutsu would confuse the machines and give Aloy an edge in combat.
One plot idea could be that Zero Two and Naruto are from different universes but are brought together by some sort of magical or scientific accident. They then have to team up to fight a common enemy that is threatening both of their worlds. Another idea could be that Zero Two somehow ends up in the Naruto world and has to adapt to its ninja culture while also using her unique abilities to help Naruto and his friends on a mission. Maybe she could even learn some ninja techniques herself.
One interesting Naruto and Zero Two fanfiction could be a crossover where Naruto visits the world of Darling in the Franxx. In this story, Naruto's skills and positive attitude might inspire the pilots, including Zero Two. He could teach them some of his ninja techniques, which would add a new dynamic to their battles against the klaxosaurs.
If Hinata were to meet Zero Two, there could be an interesting dynamic. Hinata's shy and kind nature could contrast with Zero Two's more brash personality. However, they might find common ground in their loyalty towards their respective partners (Naruto for Hinata and Darling for Zero Two). They could support each other in times of crisis and learn from each other's strengths.
One idea could be to create a crossover where Naruto characters are transported to the world of Familiar of Zero. For example, Naruto could be mistaken for a powerful familiar. Another idea is to have a character from Familiar of Zero learn ninjutsu from Naruto. Maybe a familiar in the Familiar of Zero world could have the Nine - Tails' chakra sealed within it.
One idea could be that they face a new and powerful enemy together that is a threat to their entire world. They have to combine their unique abilities in ways they've never done before to defeat it.
One idea could be a crossover of Naruto's world and the Familar of Zero world where Naruto has to learn the magic system in the new world. Maybe he teams up with Saito from Familar of Zero to fight a common enemy.
Perhaps in the fanfiction, the Zero Tails is a manifestation of the negative emotions of the ninja world as a whole. A group of young ninjas discover this and they try to find a way to purify the Zero Tails. They seek the help of old sages and learn ancient jutsu to attempt this purification, which could lead to a battle against those who want to keep the Zero Tails as a weapon of mass destruction.
One idea could be Naruto being summoned as a Servant in the Fate Zero world. His unique ninja abilities would make for an interesting dynamic against the traditional Servants. He could use his shadow clones to outnumber opponents or his Rasengan in combat.
One idea could be a crossover where Naruto characters gain the abilities of Mega Man Zero. For example, Naruto could use Zero's saber in combat, adding a new dimension to his fighting style. Another idea is a story where the world of Naruto is invaded by enemies from the Mega Man Zero universe, and the ninja have to adapt quickly to survive. Maybe even a story where Mega Man Zero is somehow transported to the Naruto world and has to learn about chakra and ninja techniques to find his way back home.