Board Thread:Naruto Discussions/@comment-28861328-20140618060932/@comment-7862945-20140618231143

Basically, this is a basic summary of what is going on.

In the series, Chakra was it's own separate energy. But people said Chakra was a mix of physical energy & spiritual energy.....

But, they only thought that way because from the moment they were born, their spirit & physical energy was already saturated with Chakra.

It being always mixed from as far back as their history goes, thus, almost nobody knew that chakra was actually a separate energy.

So the explanation of what chakra was in the beginning of the series is technically wrong (though the people can't be blamed cause their spirit & physical energy was always mixed with chakra).....

So nobody in the Naruto-verse had pure mental/spirit energy or physical/life energy, it was always mixed with the energy called chakra & the Shinju is a massive tree mixed with this energy called chakra along with a huge amount of natural energy.

Humans in their selfishness basically tried to horde this chakra energy for themselves and connected it with their physical & spiritual energies, creating the chakra known today.

Kaguya's 2 children received part of her powers. Hamura had her Byakugan to see everything, while Hagoromo got the Rinnegan.

Hagoromo's children in turn got half of his Rinnegan power. Asura got the life force and physical energy of the Rinnegan while Indra got the Ocular power and spirit energy or the Rinnegan (the Ocular and spiritual half of the Rinnegan's power was later dubbed the Sharingan).

Madara was one of Indra's descendants who has inherited Indra's power. Madara at some point, through the manipulation of Black Zetsu, to take Hashirama's DNA to complete his half of the Rinnegan (aka Sharingan) to make it into the complete Rinnegan.

Black Zetsu was a part of Kaguya's will that watched the world, and he manipulated Madara into using the Infinite Tsukuyomi, making him believe that he created the White Zetsu's which were actually people who were sealed in the Gedo Mazo under the previous Infinite Tsukuyomi. Then, Madara was tricked into believing that he created Black Zetsu.

Now Kaguya wants that energy called chakra back, not the people's life and spirit energies, but her powers.

Apparently, she created the Jubi to retrieve the energy called chakra, so she could go back to ruling the world. Watching and controlling everyone with her Byakugan & Rinnegan.

It's missing somethings, but that is basically what is going on in the story.