Disclaimer: I don't own Naruto.
His true legacy was not the village, or the memories left behind. It wasn't even the philosophy he lived up to, nor the technique he invented.
The Yondaime's legacy was a small, whiskered face with wide blue eyes, belonging to a mouth that never shut up and to a soul that, no matter what wrong was done to him, never gave up. The Yondaime's legacy was a little nobody who proved that even nobodies could do anything.
But nobody knows that. No one in Konohagakure knows that the boy they scorn, the boy they hate and fear, is all they have left of their beloved leader, and it would kill them to know the truth of what they have been doing all of those years. Not that they would believe it if they were told.
The title of kage, in any village, is essentially a promise, to die for the village. If a hidden village falls under attack, then the kage must be willing to sacrifice their life for the sake of their village, so that their village may see another day of life, to rise again from whatever ashes engulf it.
The Yondaime was willing to die for his village. But what no one remembers, what no one ever knew, was that Konohagakure was not all the Yondaime died for that night.
Fulfilling the oath he took when he accepted the office of Hokage, the Yondaime willingly gave up his life for Konohagakure the night the Kyuubi no Kitsune ravaged the village he had been raised in, not giving a second thought to the fact that what he was about to do would most likely be his death.
But that was not all he died for.
There were a million faces, a sea of faces in a throbbing crowd. But one stood out. One that was far more important than all the rest. One that the Yondaime was desperate to save, determined to save, even if the rest of his village burned.
On the night when the autumn leaves that had begun to frost with winter melted and burned, the Yondaime died for his infant son.
He died so that his son might live to see the world out of the eyes of an adult, that his son might live to see the sun for the first time with his infant eyes. The Yondaime sealed the Kyuubi inside of his infant son to save him and everyone else from the beast's rampage.
But no one remembers that. Everyone despises the Yondaime's "murderer", and never realizes that he cared much more about the boy they hate than he ever did about them.