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.
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 origin could be a genetic mutation within the Uzumaki clan that has been dormant for generations. Naruto, being an Uzumaki, could be the first in a long time to have this mutation manifest as claws. Or it could be due to a curse placed on him by an enemy. However, instead of weakening him, the curse gives him the claws which he then learns to use to his advantage. It could also be a gift from a powerful sage or spirit that he encounters during one of his adventures, seeing the potential in Naruto and bestowing him with the ability to have claws for a specific purpose like protecting the village or fighting a greater evil.
Perhaps it was a gift or a curse from some powerful being. For example, a god or a demon could have bestowed this third eye upon Naruto for some purpose, either to help him in his journey or to make his life more difficult with new powers that come with their own challenges.
In fanfiction, the origin of Naruto having 2 tailed beasts could be due to a powerful ninja's experiment. This ninja could have been trying to create a super - powerful warrior and decided to combine the power of two tailed beasts into one person, which happened to be Naruto. Or it could be a gift from some sort of god - like being in the Naruto universe. This being might have seen Naruto's potential and decided to bestow an extra tailed beast on him to help him in his future battles and challenges.
Perhaps he had an encounter with a powerful monkey - themed ninja or a mystical monkey creature. This encounter could have resulted in a transformation or a gift that gave him the monkey tail. For example, he might have saved a sacred monkey in a forest and as a reward, it bestowed upon him this unique feature.
One possibility is that it could be a result of a genetic mutation. Maybe something in his Uzumaki heritage combined with the Nine - Tails' chakra in a unique way to produce this purple chakra.
One possibility is a genetic anomaly. Maybe there was some long - forgotten connection between the Uzumaki and Uchiha clans in the past that resurfaces in Naruto. Another could be that a powerful enemy or ally uses a special jutsu on Naruto that implants the True Sharingan into him. It could also be a result of Naruto's own experimentation with chakra manipulation in his quest to become stronger.
In some fanfictions, it could be a result of a new jutsu he developed. Maybe he combined his chakra control with some ancient fire - based technique he discovered, leading to the ability to breathe fire.
Well, it might be the result of a powerful curse or a blessing from a god - like being. In the Naruto universe, there are many powerful entities. If one of them decided to bestow this unique power on Naruto, it could lead to the development of the red Rinnegan. Another idea is that it could be a side - effect of a new jutsu he tries to master. Some jutsus have unforeseen consequences, and this could be one of them.
It could be a result of a magical experiment gone wrong. Some rogue ninja or a mad scientist - type character in the Naruto universe might have been trying to create a super - being and accidentally gave Naruto red angel wings.