Maybe it's some kind of experimental jutsu gone wrong. Some rogue ninja or a mad scientist - type character could have been experimenting on Naruto, and as a result, he ended up with six arms.
It could be a curse. Perhaps Naruto angered an ancient and powerful being, and as a punishment, he was cursed with six arms. This would add an interesting plot element to the fanfiction, as Naruto would have to find a way to break the curse while dealing with the challenges of having six arms.
Well, having six arms would give Naruto more options in combat. He could use multiple jutsus simultaneously. For example, he could form Rasengan in three hands while using shadow clones with the other three to distract his opponents. This would make him more unpredictable and powerful in battles.
In the fanfiction, the origin of Naruto having six eyes might be related to a special training or a forbidden jutsu. He could have stumbled upon an ancient training ground where he was exposed to some sort of energy or knowledge that granted him the six eyes. Or maybe he was forced to use a forbidden jutsu to save his friends during a critical battle, and as a side effect, he got the six eyes.
One possible aspect could be that in fanfiction, Kidomaru's six arms might be used in a very unique way in relation to the sakura. For example, he could use his multiple arms to perform some sort of special dance or ritual among the sakura trees. This could be a part of a cultural or spiritual event within the fan - created world. Maybe his six arms give him an advantage in collecting sakura petals for some magical purpose, like creating a powerful potion or a charm that is related to the beauty and transience of the sakura.
One possibility is that this encounter is a result of a misunderstanding. Kidomaru might mistake Sakura for someone else and pins her with his six arms. Sakura, in shock, has to quickly figure out how to communicate with him to clear the confusion.
The six arms could be used for combat in a sakura - themed setting. He might use them to swing from sakura branches, using the trees as a sort of battlefield advantage. His arms could also be used to grab and throw sakura - covered boulders or other objects at his enemies.
I'm not sure specifically as I haven't read this exact fanfiction. But generally, it might involve Sakura facing various challenges or difficulties while in the situation related to Kidomaru's six arms. It could be about her trying to overcome physical battles or dealing with emotional turmoil in that particular fan - created scenario.
Obviously, Sakura and Kidomaru are the main characters. Sakura is the one who is struggling, and Kidomaru with his six arms is the source of the struggle.
In such a fanfiction scenario, it could be a very intense situation. Maybe Kidomaru uses his six arms to physically restrain Sakura. This could lead to a fight where Sakura has to use her medical ninjutsu skills in a more combat - oriented way to break free. For example, she might use her chakra enhanced strength to push Kidomaru's arms away.
In some Naruto fanfictions, chakra arms can be used for enhanced combat. For example, they can be extended to strike enemies from a distance. They might also be used to grapple and throw opponents with great force, similar to how Naruto sometimes uses his shadow clones for creative combat maneuvers.
Three heads and six arms were the special abilities of the legendary character Nezha.