Well, in this kind of fanfiction, Naruto might use his powerful jutsu to influence political situations across the ninja world. He could impose his ideas of peace on all the hidden villages, uniting them under his leadership through sheer force and charisma.
It could be some of the traditional power - hungry ninja clans who oppose Naruto's new world order. They might see his attempts at global control as a threat to their own interests and try to undermine him.
Foxes are quite common. Given Naruto's connection with the Nine - Tailed Fox, it makes sense that in fanfiction, he might be able to control other foxes. They can be used for scouting or as distractions in battles.
One idea could be that Naruto discovers a strange new chakra within the headcrabs. He then figures out how to manipulate this chakra to control their actions. He might train them to perform tasks like scouting or even to help in rebuilding damaged villages by using their physical strength.
Crows are also often seen. Crows are intelligent and can be used for spying or sending messages. Naruto in fanfiction might control them to gather intelligence on his enemies. And they can be very stealthy, flying around unnoticed most of the time.
In this fanfiction, Naruto's ability to control shadows could be related to his connection with the Nine - Tails. Maybe the power of the Nine - Tails unlocks this new ability within him. He could use the shadows to form shields against attacks, or even to travel quickly from one place to another by using the shadows as a sort of transportation network within the ninja world.
The Akatsuki members might also be antagonists. Since they're after the tailed beasts, Naruto with his additional power of lightning control would be a prime target. They might send their most powerful members like Pain or Itachi to deal with him.
Well, it could be about Naruto using his chakra to control paper in unique ways. Maybe he creates paper constructs for battle or uses it to send secret messages.
In a 'Naruto controls necromorphs' fanfiction, Naruto would bring his own set of values from the Naruto universe. His sense of justice and protection might lead him to try and use the necromorphs for good, like using them to protect a village or an area from other threats. However, he would also have to deal with the fact that necromorphs are grotesque and often uncontrollable creatures in their own right.
Obviously Naruto would be the main character as he has the power to control vacuums. His friends like Sasuke and Sakura could also be involved. Sasuke might be skeptical at first about this strange new ability of Naruto's. Sakura could be trying to find a scientific explanation for it, thinking it has something to do with Naruto's unique chakra nature.