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So I've been working on a theory, which by the way is probably obvious to a lot of people but I felt the need to put it all together in a simple thread, that and I was bored :3 Please take the time to read! 
So anyway, we know that the Sage of Six Paths fought the Juubi and sealed it within his own body. It's not apparent whether the sage had Rinnegan BEFORE he fought the Juubi or AFTER (my guess is before due to him being shown with it in his various silhouette's but you never know). We also know that the Juubi possesses some form of Dojutsu that resembles something like the Rinnegan and Sharingan combined. My theory begins with the Sage somehow being CONNECTED to the Juubi in some way. Depending on whether you believe he got the Rinnegan before or after his confrontation with the Juubi would alter this theory slightly but whatevs.
In short, the Sage managed to receive/steal/gain his power from the Juubi in some way and became the first ninja to use chakra in the way that all ninjas do.
This leads us to the next bit. His sons.
It's a common fact that the Sage had two sons, and one inherited his EYES (Sharingan and with a little wood, Rinnegan) and one got his BODY (the Senju).
We know a lot about Sharingan descendants via Sasuke, Madara, Itachi, Trollbito etc. but what do we know about the Senju who inherited the Sage's body? Well who comes to mind when the Senju are brought up?
That's right, the man with the wood, Hashirama. The so called God of Shinobi was, so far as we know, the greatest Wood-Style user ever and did a lot of amazing things in life thanks to it. Furthermore, his CELLS (key part) can be used in a variety of ways to strengthen certain jutsu's, prolong life and other crazy things. This is because Hashirama was able to bring out the Senju cells full potential and hence, why everyone is so crazy about his DNA.
So here's the theory. The CELLS of the Juubi is comprised of Wood-Style elements, and since the Sage somehow inherited the Juubi's powers, he was able to pass on the powers of the Juubi (both Sharingan and Senju DNA) in human form to create all ninjas and ninjutsu. Wood Style is so effective against the Tailed Beats because it came from the Juubi itself. What recent proof do we have?
Here we see the Juubi using Wood Style.
Here we see Hashirama grabbing a TB Bomb, wood style seems to render them ineffective (they don't blow up).
The Juubi flicks a TB Bomb like it's a booger.
Here we see Yamato binding Foxed Naruto with his Wood-Style Jutsu
Here we see Obito comment on the Juubi's "strong" exterior.
Obito (with Senju DNA/a half-Zetsu body) takes a hit from a Kurama (a Tailed Beast) Mode Naruto and doesn't get his head blown off.
Furthermore, the Gedo Mazo (the SHELL of the Juubi) and the cultivation of Hashirama's Senju cells allowed for Zetsu to be born. The reason Black Zetsu claims he is the land itself is because he came from the Juubi, a nature deity.
Hashirama's cells also allowed Obito and Madara to utilize wood style techniques as well as granting Madara the Rinnegan and Obito to also use it. The reason why you need both Uchiha and Senju portions to unlock the Rinnegan and use techs like Izanagi is because these are techs that originate with the Juubi (which as a whole already possesses the powers of the Uchiha and Senju).
TL;DR: The Juubi is a NATURAL ENTITY (uses Natural chakra) so in a sense you could say the Juubi was the first natural non-human ninja to use supernatural powers. The Sage of Six Paths (first Ninja) somehow humanized the Juubi's powers into human form. These powers were divided into the Sharingan of the Uchiha, and the Cells of the Senju. From the two sons, a dilution occurred and various forms of ninjutsu branched out from them over time leading to the variety of ninja that exist today.
I personally believe that the Sage was an Uzumaki and hence the link to Naruto, but whatever you like ;3 What do you guys think?
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So anyway, we know that the Sage of Six Paths fought the Juubi and sealed it within his own body. It's not apparent whether the sage had Rinnegan BEFORE he fought the Juubi or AFTER (my guess is before due to him being shown with it in his various silhouette's but you never know). We also know that the Juubi possesses some form of Dojutsu that resembles something like the Rinnegan and Sharingan combined. My theory begins with the Sage somehow being CONNECTED to the Juubi in some way. Depending on whether you believe he got the Rinnegan before or after his confrontation with the Juubi would alter this theory slightly but whatevs.
In short, the Sage managed to receive/steal/gain his power from the Juubi in some way and became the first ninja to use chakra in the way that all ninjas do.
This leads us to the next bit. His sons.
It's a common fact that the Sage had two sons, and one inherited his EYES (Sharingan and with a little wood, Rinnegan) and one got his BODY (the Senju).
You must be registered for see images
You must be registered for see images
We know a lot about Sharingan descendants via Sasuke, Madara, Itachi, Trollbito etc. but what do we know about the Senju who inherited the Sage's body? Well who comes to mind when the Senju are brought up?
You must be registered for see images
That's right, the man with the wood, Hashirama. The so called God of Shinobi was, so far as we know, the greatest Wood-Style user ever and did a lot of amazing things in life thanks to it. Furthermore, his CELLS (key part) can be used in a variety of ways to strengthen certain jutsu's, prolong life and other crazy things. This is because Hashirama was able to bring out the Senju cells full potential and hence, why everyone is so crazy about his DNA.
So here's the theory. The CELLS of the Juubi is comprised of Wood-Style elements, and since the Sage somehow inherited the Juubi's powers, he was able to pass on the powers of the Juubi (both Sharingan and Senju DNA) in human form to create all ninjas and ninjutsu. Wood Style is so effective against the Tailed Beats because it came from the Juubi itself. What recent proof do we have?
Here we see the Juubi using Wood Style.
You must be registered for see images
You must be registered for see images
You must be registered for see images
You must be registered for see images
You must be registered for see images
You must be registered for see images
Furthermore, the Gedo Mazo (the SHELL of the Juubi) and the cultivation of Hashirama's Senju cells allowed for Zetsu to be born. The reason Black Zetsu claims he is the land itself is because he came from the Juubi, a nature deity.
You must be registered for see images
Hashirama's cells also allowed Obito and Madara to utilize wood style techniques as well as granting Madara the Rinnegan and Obito to also use it. The reason why you need both Uchiha and Senju portions to unlock the Rinnegan and use techs like Izanagi is because these are techs that originate with the Juubi (which as a whole already possesses the powers of the Uchiha and Senju).
TL;DR: The Juubi is a NATURAL ENTITY (uses Natural chakra) so in a sense you could say the Juubi was the first natural non-human ninja to use supernatural powers. The Sage of Six Paths (first Ninja) somehow humanized the Juubi's powers into human form. These powers were divided into the Sharingan of the Uchiha, and the Cells of the Senju. From the two sons, a dilution occurred and various forms of ninjutsu branched out from them over time leading to the variety of ninja that exist today.
I personally believe that the Sage was an Uzumaki and hence the link to Naruto, but whatever you like ;3 What do you guys think?