One idea could be exploring their relationship against the backdrop of the ninja world's politics. Maybe they have to keep their relationship a secret while dealing with the various power struggles. For example, Itachi could be using his position in the Akatsuki to protect Naruto from certain threats, all while their feelings for each other grow deeper.
One idea could be that during their time travel, Naruto and Itachi end up in a time when the Uchiha clan was not massacred yet. Itachi has to face his past self and Naruto tries to find a way to prevent the tragedy without changing too much of the future. Another plot could be that they travel to a future where everything is in chaos and they have to use their combined skills and new - found relationship to set things right.
One idea could be a story where Hidan and Itachi are forced to work together on a mission. They start off disliking each other but gradually, through shared experiences and understanding, they develop feelings for one another. It could explore how their different personalities, Hidan's brashness and Itachi's calmness, create an interesting dynamic.
One idea could be exploring a time - travel scenario where child Naruto somehow gets to interact with Minato in a different way than in the original story. Maybe Naruto's childlike innocence changes Minato's perception of things. Another plot could be centered around Naruto learning about his father through a magical bond that has yaoi undertones, like they can communicate in their minds and feelings start to develop.
One idea could be that Naruto discovers Itachi's true motives early on. So instead of seeing him as an enemy, he tries to help Itachi with his mission in the Akatsuki secretly. They could meet in secret places and exchange information about the Akatsuki's plans and how to protect the Leaf Village at the same time.
One idea could be Itachi discovers Baby Naruto has a unique chakra signature that could change the future of the ninja world. So, he decides to secretly protect Naruto from afar. Another could be Itachi is tasked with a mission that involves Baby Naruto in some way, like having to test Naruto's potential without the village knowing. And a third could be Itachi has a vision of a future where Baby Naruto is the key to peace, and he starts to subtly influence Naruto's growth even at that young age.
A possible plot could involve Female Itachi being an outcast in her own clan because she has different ideals. Naruto, who always believes in people, befriends her. They then start a journey to prove that her ideas can bring peace to the ninja world, facing opposition from both their own and other clans.
One idea could be a story where baby Itachi meets a young Naruto in a sort of alternate universe. Maybe Naruto stumbles upon a hidden place where baby Itachi is being kept safe. They form an unlikely friendship, and Naruto's positive energy starts to influence Itachi in a way that makes him question some of the darker paths he might take in the future.
One idea could be exploring Itachi's time in ANBU and how Naruto might have influenced his decisions secretly. Maybe Naruto, with his unique way of seeing people, could have made Itachi question his path in the ANBU more deeply.
One idea could be that the Kyuubi's power somehow interacts with Itachi's Sharingan in a unique way. Maybe Itachi is able to use the Kyuubi's chakra to enhance his genjutsu even further. Another plot could involve Naruto, with the Kyuubi inside him, teaming up with Itachi to face a common enemy that neither could defeat alone. For example, a new powerful Otsutsuki clan member arrives, and their combined skills are needed to save the village.
Maybe a fanfiction where Konan discovers a secret about Itachi that could change the way Naruto views him. This could lead to a complex web of relationships and a journey of self - discovery for Naruto as he tries to figure out who to trust. The story could also explore Konan's past more deeply in relation to this new discovery.