I like Breaking Bonds, but I think Sacred Grounds would help to explain
why you're limited to picking one of two chakra natures per village
when starting out- It's because the natural chakra inherent in the land
influenced it at your birth. Those who have kekkei genkai have "Inherited"
the land's gift more prominently.
The first however, would explain where we get Kenjutsu from-
The teachings of the first Samurai who wielded chakra-enhanced swordplay.
Currently existing clans who have a strong samurai vibe to them could be
explained as having been influenced by this history.
And Sacred Grounds could explain how these uncontrollable abilities developed-
these were simply individuals who had "Inherited" it from their homelands.
The cloaked individual in Gifted Abilites is the scientist who expirimented on children in Expirimentation,
and who is offering to forcefully alter the genes of clans,
enabling their descendants to have a better chance of "Inheritance".
Inheritance. That is a seriously bitching name to call it.
So: A long time ago there was a giant shogunate.
There were only Samurai who used chakra for their kenjutsu.
Certain areas in the land were prone to releasing Chakra,
which could alter the flora, fauna, and people who inhabited them.
Sometimes people very rarely were born strongly connected
to this chakra.
Like Rising Moon, a boy who was born in what would eventually become Kazangakure,
currently known as the Land of Sulfur.
Due to the land overflowing with flaming, earthy chakra,
he was born with a Fire in him. When he was 12, he noticed that when his
emotions became unstable, things burned as he touched them. He struggled to control this,
afraid of how people would react. But eventually he was found out, and taken before the shogun.
He was put with others like him, overflowing with natural chakra, to be trained.
Eventually, he unlocked the potential to wield earth as well.
These would become sevenfold stronger over the course of his life.
Part 2 (Takes place decades after shinobi clan's uprising as explained in Breaking Bonds)
Yokaze was a scientist from the Land of Crows who had kidnapped certain children,
descendants of a direct line born from Rising Moon himself.
He had expirimented on them, and though it had required their deaths,
he'd found a way to implant Rising Moon's potential in other shinobi born in the Land of Sulfur.
He took his work to the current leader there, and offered to forever alter certain individuals,
giving their children a chance to become strong.
New people born, like Rising Moon, had more access to the natural chakra of the land,
which meant more people would be born shinobi.
(This explains why you have to pick either Earth or Fire as your primary nature in Kazangakure.)
Eventually, some children who were born with Rising Moon's original natures,
Fire and Earth, displayed a unique ability Rising Moon had not had-
They could combine their natures, creating magma,
Much like how the earth combined heat and stone.
Yokaze decided to call this power "Inheritance".
We can also replace "Kekkei Genkai" with this,
like how you changed "Chidori" to "Lightning Ball".
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