It is said that Bongo Bongo was an ancient thief whose hands were cut off and his head decapitated. After this incident, he was buried under his house, which was then walled up.
The Kakariko's Well was built at its former entrance but When Ganondorf gained his power, he wreaked havoc on the village, awakening the man's spirit. After this, the spirit escaped to the village and hid in the Temple of Shadows.
You entered into the Temple of Shadows, the temple was filled with undead creatures, deadly twisted traps, and mind-bending puzzles everywhere... all designed to trap anyone who enters the crypt. It was also filled to the brim with invisible walls and passageways. Many concealed Skulltulas hang in rooms and corridors within the temple's walls.
You were getting deeper... and deeper... and deeper... arriving to the basement of the Temple, that was dim-lighted, with a great hole in the middle of this.
You enter into this hole, falling on a giant bongo drum-like platform, surrounded by poisonous green gunge. All was surrounded by darkness but sudently...
A a large, dark hands bangs on the drum-platform that you were standing as other hand appears and joins the banging, both hands were beating the drum with a execution rhythm... you look above and there he was...
Bongo Bongo's giant body was hanging from the celling, staring at you with that big red, glowing eye as it's "head" before it fades into the darkness of the room.