He was a young boy when he had first met Navi. He had only looked the part when Navi—for whatever reason—had left him.
Why? Link had wondered, as he watched her slowly flutter away.
Navi meant a lot to him. She was his one, true companion in the dark, corrupted world that he had let Ganondorf create in his absence. Navi was a constant. She was always there for him; she was always ready to watch over him, to protect him, to care for him, to—
Maybe that was why Navi had left him. Adults didn't need parents.