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 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.
It could be a symbol of a new power. Maybe it gives Naruto the ability to control scorpion - related things, like scorpion - shaped chakra attacks.
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.
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.
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 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 possibility is that it could be a genetic anomaly. Maybe something in his Saiyan genes that was dormant suddenly activated, causing the tail to grow back. In the Dragon Ball universe, Saiyan genetics are complex, and there could be some unexplored factors at play.
One origin could be a curse placed on Naruto. In the Naruto universe, there are many powerful curses. This curse could be related to the nine - tailed fox's history or some ancient feud. It might be that a long - forgotten clan or entity has put this curse on Naruto as a form of revenge or to serve their own dark purposes. Or it could be a natural evolution of Naruto's connection to the nine - tailed fox as he reaches a new level of power, but his body isn't fully able to handle it yet, so it manifests in these physical changes.