In fanfiction, a Naruto magic staff could have the power to control the elements more precisely. For example, it might enhance fire - style jutsu to a greater degree than normal chakra control allows, making the flames hotter and more destructive.
It could make Naruto overpowered. If he gets the magic staff early on, battles that were supposed to be tough in the original story might become too easy for him. For instance, against Orochimaru, he could just use the staff's power to nullify Orochimaru's jutsu and defeat him quickly.
Naruto could use the staff to gain new powers. For instance, he might be able to fly or teleport using the staff's magic. It could also be a key to unlocking some ancient ninja secrets. Maybe it reveals the location of a long - lost ninja village.
His hidden powers might be the ability to control all five basic nature types without any training. In the original story, Naruto had to work hard to master different nature types. But in a fanfiction, it could be that he has this innate ability which was hidden all along. This would make him extremely powerful and feared by his enemies.
The plot could be that Shikamaru is the only one who can master the Shadow Staff Wave due to his unique chakra control. He is then targeted by an evil organization that wants to use his power for their own malicious purposes. Shikamaru has to fight against them while also trying to understand the true potential of the Shadow Staff Wave.
One plot idea could be that the Staff of Shadow has a hidden prophecy. Shikamaru discovers this and Naruto helps him figure out what it means. Maybe it foretells a great danger to the Hidden Leaf Village, and they have to use the power of the staff to prevent it.
It might have the power of transformation. For example, Percy could use it to turn into a snake - like form, which would give him new abilities like slithering through small spaces or having a heightened sense of smell.
Maybe it's some kind of ancient bloodline that was dormant in his family for generations. It suddenly became active in him.
One possible power for Naruto as a descendant of a god in fanfiction is the ability to communicate with all living things. This would give him an edge in gathering information and in forming alliances. He could also have a special form of chakra that is far more potent than regular chakra, enabling him to perform jutsus that are otherwise impossible.
Naruto might be able to use Medusa's powers in creative ways during his missions. For example, he could use it to immobilize traps. If there was a trap with moving parts, he could turn those parts into stone, disabling the trap. Also, he could use it on secret passages to block off pursuers by turning the entrance or the passage itself into stone.
Well, if Naruto had Shego's powers, he would gain some interesting abilities. Shego has the power of green energy blasts which Naruto could use in combat. He might use them in combination with his shadow clones. For example, while the clones engage the enemy in close combat, he could use the energy blasts from a distance to surprise the opponents. Also, Naruto's already acrobatic fighting style could be enhanced with Shego's powers, making him even more unpredictable in battle.