Perhaps it was a gift from a powerful entity. There could be a god - like being in the fanfiction who decided to bestow Naruto with the ability to see chakra. This entity might have seen Naruto's potential and believed that this ability would help him in his journey to protect the village and become a stronger ninja.
It could be the result of some kind of special training. Maybe he met a hermit who taught him a unique technique to perceive chakra in a visible way. For example, this hermit might have had him meditate in a special chakra - rich area and gradually opened his eyes to the world of visible chakra.
Another possibility is that it's a genetic mutation. Since Naruto has the Nine - Tails inside him, it might have somehow affected his chakra perception abilities. The Nine - Tails' powerful chakra could have interacted with Naruto's own, evolving his senses to be able to see chakra. This would be an interesting twist on his character development.
Well, Naruto's ability to see chakra can give him a huge advantage in combat. He can easily detect an opponent's chakra flow and predict their moves. For example, if an enemy is gathering a large amount of chakra in their hands for a powerful attack, Naruto can see it and dodge or counter - attack before the attack is launched. This allows him to be more proactive in battles instead of just reacting to his opponent's visible actions.
It might be a result of some special training or encounter. For instance, if Naruto had a unique experience during a mission or while training with a new mentor, this could have triggered the unlocking of the chakra chains. It could be that he tapped into a new source of chakra or learned a new technique that enabled this ability.
One possible origin could be a long - lost kekkei genkai. Maybe Naruto's family had a secret bloodline ability that was suppressed for generations, and now it resurfaces as the red chakra.
It could be due to a unique training method. In fanfiction, perhaps Naruto discovered a new way to purify his chakra through intense meditation or some sort of elemental training that no one else has tried before.
In some fanfics, Naruto's chakra chains could be a result of some ancient Uzumaki clan ability that he discovers. Maybe it was a hidden power within his bloodline all along, and through intense training or a particular encounter, he unlocks this ability to use the chakra chains.
Perhaps the origin of the chakra chains lies in Naruto's connection to the tailed beasts. Since he has a unique bond with the nine - tailed fox, the chakra chains might be a manifestation of that bond, combined with his own latent Uzumaki powers. It's possible that as he grew stronger and his understanding of chakra deepened, this ability was awakened.
It could also be a part of his training or self - discovery. Naruto might have realized that he was relying too much on his chakra and wanted to find a new way to be strong. By sealing off his chakra, he could focus on other aspects like his physical strength, strategic thinking, or even his ninja skills without the use of chakra.
Naruto might also go through an identity crisis. His whole life has been centered around being a ninja with chakra and using powerful jutsu. Losing his chakra could make him question who he is and what his purpose is. He would have to redefine himself and find a new way to contribute to the ninja world. This could be a long and difficult process for him.
One consequence could be that he becomes extremely powerful. His physical abilities like strength, speed, and endurance are enhanced. He can also use more powerful jutsus with the extra chakra boost from the Kyuubi.
One interesting way is when Naruto absorbs chakra through his shadow clones. In some fanfictions, the clones can be used not just to gather information or attack, but also to absorb the chakra of the opponents they interact with. Then, they transfer this absorbed chakra back to Naruto, making him more powerful.