One possible plotline could be Naruto somehow obtaining the powers of Doctor Fate and using them to protect the Hidden Leaf in a different way. Maybe he uses Doctor Fate's magic to fight against threats that normal ninja techniques can't handle.
A plotline might involve Naruto being transported to the world of Doctor Fate. There, he has to learn how to use Doctor Fate's powers while also dealing with the new environment and its challenges. He could form new alliances and enemies in this strange new world.
Perhaps in the fanfiction, Doctor Fate's helmet chooses Naruto as its new wielder. Naruto then has to balance his ninja life with his new role as Doctor Fate. He might use his ninja values like loyalty and perseverance along with Doctor Fate's powers to combat villains that are after the power of the helmet. This could lead to some epic battles and moral dilemmas as Naruto tries to figure out how to use his new powers for good without losing his own identity.
One possible plotline could be the characters from Kekkai Sensen getting involved in the Holy Grail War from Fate. Maybe they are summoned as Servants or they interfere with the war for their own reasons. Another could be the Fate characters ending up in the world of Kekkai Sensen and having to deal with the strange creatures and the kekkai barriers there.
A possible plotline could be that Calypso, with her alluring powers, tries to tempt Naruto away from his path of becoming Hokage. But Naruto, with his strong will, resists and instead tries to show Calypso the importance of having a noble goal. Another plotline might be that Naruto and Calypso team up to fight a powerful entity that is causing chaos in both their worlds.
One possible plotline could be Naruto using his new position as a daimyo to bring about political reform in the ninja world. He might try to end the long - standing feuds between different ninja villages by leveraging his power.
One possible plotline could be that Naruto dies during a great battle, like against Kaguya. But his spirit remains because he has some unfulfilled desires, like seeing the village fully at peace. So, as a ghost, he tries to influence the living to achieve that peace.
A possible plotline could be Orochimaru's redemption. He realizes the error of his ways and joins Naruto in protecting the ninja world. He could use his vast knowledge of jutsu and forbidden arts to help Naruto against new threats.
One plotline could be Naruto starts in his own world, discovers a portal to the Pokemon world, and decides to explore it. He might start as a novice Pokemon trainer and quickly rise in the ranks using his ninja skills.
One plotline could be that Naruto is chosen by Poseidon to be his champion in the human world. He is given special powers to protect the seas and their secrets from those who would misuse them. Naruto, with his determination, uses these new powers to fight off evil forces that are threatening the ocean's balance.
One plotline could be Naruto starting from the bottom in the wrestling world. He's underestimated because of his small stature or his goofy personality, but he quickly rises through the ranks with his unique fighting style that combines ninja moves with wrestling holds.
One plotline could be that Aphrodite takes an interest in Naruto because of his pure heart. She decides to bestow some of her powers on him, which gives him a new ability related to charm or attraction. This could be used in his battles, not in a traditional sense of a weapon, but more like a way to disarm his opponents mentally. For example, he could make his enemies hesitate or become distracted by his newfound allure.
In a 'naruto is a alien fanfiction', a plotline could be that Naruto is the last of his alien kind, and there is a powerful enemy that is after the secrets locked within his DNA. As he tries to protect himself and those he loves, he discovers new powers related to his alien side. He also has to deal with the prejudice from some in the ninja world who fear his alien nature, all while trying to use his new - found powers for good and save the day.