You could start with a plot where the Saiyan race is somehow connected to an ancient shinobi clan in the Naruto world. A young Saiyan - Naruto hybrid discovers this connection and is then drawn into a conflict that requires the help of the Avengers. Maybe there's a powerful enemy that wants to use the combined power of Saiyan and ninja abilities for evil, and the heroes must stop it.
Create a plot where a group of villains from both universes team up. The Saiyan villains from Dragon Ball and the powerful enemies from Naruto join forces. The Avengers and Naruto characters then form an alliance. As they fight, they discover that the source of the villains' power is a corrupt form of chakra that can only be purified by a combination of Saiyan energy and the purest form of ninja chakra. So, they embark on a journey to find this purification method while also fending off the villains' attacks.
For a unique plot, consider a scenario where the Infinity Stones are actually fragments of a powerful chakra - based artifact from the Naruto universe. The Avengers and Naruto characters must work together to prevent a dark force from reassembling these stones/artifacts. Along the way, Naruto and some of the Avengers learn to transform into a new, combined form that gives them the strength to face the threat. This form could be a mix of Super Saiyan and Sage Mode, for example.
You could start with the idea that the Monopoly game is a training exercise created by a powerful ninja. The players have to not only win the game but also learn valuable ninja skills along the way. For example, if they pass 'Go', they gain a new jutsu instead of just getting money.
You can start by focusing on a side character from the original series and build their story in the future. For instance, Rock Lee's son could struggle with not having the same natural talent as his father but overcomes it through sheer determination and a new form of taijutsu training.
Combine the ninja clans in Naruto with the Sith hierarchy. For instance, make a particular clan have a secret connection to the Sith. This could lead to internal power struggles within the clan as some members are tempted by the Sith ways. The main character, like Naruto, could be caught in the middle, trying to save his friends from this new dark influence.
One idea could be a crossover where Naruto gains Saiyan powers and teams up with the Avengers. He could use his newfound Saiyan strength and speed, combined with his ninja skills, to take on powerful villains. For example, against Thanos, Naruto could use his Rasengan enhanced with Saiyan ki energy.
Mix the power systems. Let characters combine their ninjutsu with Honkai powers in unexpected ways. For example, a character could use a water jutsu along with the Herrscher of Ice's powers to create super - powerful ice attacks.
A unique plot could involve a mix of the two worlds' magic systems. For instance, combine the Kuroinu's dark magic with Naruto's ninjutsu. The characters could learn from each other. Say, a Naruto character learns a dark magic spell and has to control its corrupting influence while using it for good.
You can make it unique by introducing a new character who is the catalyst for the yandere harem. For instance, a foreign princess with yandere tendencies visits Konoha and immediately falls for Naruto. Her presence makes the existing female characters in Naruto's life feel threatened, and they also become more yandere - like in response.
To create a unique fanfiction, focus on the less explored aspects of the Sharingan. For example, you could write about the Sharingan's influence on the user's dreams. Maybe an Uchiha character starts having prophetic dreams because of their Sharingan and it leads them on a different path in the story.
Set your story in a unique location within the Naruto universe that has been affected by the presence of ghouls. This could be a village on the outskirts that has to deal with neglected ghouls. You can explore how the local culture and ninja way interact with these strange beings, and how the characters grow in this complex environment.
One idea could be a Saiyan character having to control their power during the Chunin Exams. For example, they might accidentally release too much of their Saiyan strength during a fight, which could lead to unforeseen consequences like accidentally destroying part of the exam arena. Another plot could involve a Saiyan trying to master a new jutsu that combines Naruto - style ninjutsu with Saiyan energy blasts. This would add an interesting twist to the traditional Chunin Exams as other characters would be both amazed and a bit scared of this new power.