I think Hinata could be an ally. She has always been in love with Naruto and would not stand by while he is in danger from Dark Naruto. Additionally, Shikamaru is smart and strategic. He might see the threat of Dark Naruto to the village and decide to assist Naruto, using his intelligence to come up with battle plans.
There's also 'The Bond of Enemies'. In this fanfic, Pain, after his defeat, is given a second chance at life by Naruto. It shows a really interesting dynamic as Pain tries to figure out his new place in the world with Naruto's influence. It has some great action scenes and emotional moments.
It could be about Naruto having some sort of connection to Pain. Maybe in this fanfiction, Naruto is somehow related to Pain in a way that wasn't in the original story, like being his son in an alternate universe. This could lead to a whole new set of storylines, with Naruto perhaps having to deal with the legacy of Pain while also following his own path as a ninja.
In fanfiction, the Rinnegan is often depicted as more powerful than the Sharingan in many ways. The Rinnegan has abilities like the Six Paths techniques which can be extremely overpowered. For example, it can allow the user to control gravity, summon large creatures, and even revive the dead. While the Sharingan has its own set of cool abilities like predicting movements and casting genjutsu, it seems limited in comparison when it comes to the grand scale of power shown by the Rinnegan in most fanfictions.
In a fanfiction, the aliens could capture Naruto and try to study his unique abilities. The monsters then decide to rescue him because they realize his powers could be the key to defeating the aliens once and for all. The story could involve a lot of action as the monsters infiltrate the alien base to save Naruto.
Well, sometimes in 'naruto vs dark naruto fanfiction', a cool plotline is when Dark Naruto has some new powers that Naruto has to figure out how to counter. For example, Dark Naruto might be able to control shadows in a way that Naruto has never seen before. Or perhaps Dark Naruto has allied himself with a powerful dark force from outside the ninja world. Naruto then has to not only battle his dark self but also this new threat.
In a fanfic where Naruto gets killed by Pain, it's a dark turn of events. The story would then likely focus on how the remaining characters cope. For example, Kakashi might feel a great sense of guilt for not being able to protect Naruto. Hinata would be heartbroken. Moreover, the Nine - Tails would be left without a host, which could also lead to all sorts of problems. The ninja world would lose its most prominent symbol of perseverance and friendship, and it would be a very different world from the one we know in the original Naruto story.
Obviously, Naruto would be one of the main characters as it's about him being the son of Pain. Pain himself would also be a crucial character, even if he might not be physically present all the time. And characters like Sasuke, Sakura, and Kakashi would still likely play important roles as they are Naruto's friends and mentors in the original story and would have to interact with Naruto in this new, changed scenario.
A fanfiction titled 'Naruto's Admiration for Pain' is also worth checking out. It focuses on Naruto's growing admiration for Pain's power and ideology. However, Naruto also tries to change Pain's more extreme views. The story is full of intense dialogues and Naruto's internal struggles.
One common theme is self - improvement. Both Sakura and Naruto are constantly striving to get better in these fanfics. For example, Sakura might be trying to improve her combat skills to be on par with Naruto. Another theme is friendship. Despite their rivalry, their underlying friendship is often explored. It shows that they can compete and still care for each other.