Bongo Bongo

Phantom Shadow Beast: Bongo Bongo is a mysterious cyclopean shadow spirit with two large disembodied hands. Once sealed deep in the darkness of the Kakariko Village Well, it is unknown the true origin of the beast. Once Ganondorf came to power, the beast was able to escape its prison within the well and retreat to the Shadow Temple, where Impa went to try to seal it again.

Bongo Bongo is noted as being one of the strangest bosses in the Zelda series. Some features that contribute to its oddity are its abilities to become invisible, to sink into a shadow and travel across surfaces, and to manifest itself as a mysterious dark energy. Despite its hands being separated from the main body, it still retains full control over them from a distance, allowing the creature to punch, slap, grab and squeeze the life out of its victims. It also can shield its susceptible red eye by folding the flaps over it. It is also thought by some to be the hardest boss in the game, even harder than Ganon. It has apparently caused many people to give up the game, due to its difficulty.

When Link encounters Bongo Bongo, the battle occurs on a giant drum (most likely a Bongo, given the name) surrounded by a very poisonous purple slime (best to be avoided). Not only does it beat on the drum, but the creature sings throughout the battle with a strange voice much like the Four Giants in Termina.

If you play the game normally, it is the penultimate Temple boss to cross your path.

To defeat this beast, equip the Lens of Truth when it becomes invisible in order to see it, and avoid its hands when they attempt to attack you. Stun its hands with arrows to force it to reveal its giant eye protected by the flaps. Aim and shoot the eye with another arrow before Bongo Bongo tries to ram into you, then hack the eye with your sword. Once you repeat this process enough times, this evil will be no more.

Special: The ice arrow will also freeze a hand if hit.

A tip while facing Bongo Bongo, use your Hover Boots that you received from this temple to avoid being bonked back and forth from the drum.

Misc
There is some speculation regarding Bongo Bongo's appearance being somewhat similar to that of the Twili. Nothing can be known for sure, though there are some arguments against this since it is explicitly being told that Bongo Bongo was sealed inside the Kakariko Well and not inside the Twilight Realm.

It is also thought by many fans that Bongo Bongo is also a Shape Shifter, allowing him to take on any form, and that the one Link fought him in was just one of many that he chose from. The form Link sees him escaping from the well in (with Sheik while the village is in flames) is his "true form". Nobody knows for sure. This is merely fan speculation. It has an appearance slightly similar to Gohdan, and it is probably based on a mutated Wallmaster.

An elderly Person in Kakariko Village (located near the Spider House) tells of how a man had the ability to see the truth, and his house was where the well is today. It is possible that Bongo Bongo is this person, as he manifests himself as having one great red eye, and the Lens of Truth is needed to see him. If Bongo Bongo is this man, then it is possible that the man was executed for some reason, given that the creature's hands are separated with stumps showing the flesh of his arms, and that his head is missing, replaced by a stump with the eye supposedly being his neck. He may have been executed for being a murderer, as both the Shadow Temple and Bottom of the Well are filled with undead and have various torture devices. Bongo Bongo may have been a powerful Sheikah (as the Lens of Truth, which is related to the Sheikah, is in his house. And he inhabits the Shadow Temple) who went mad and killed several people. The Sheikah then executed him, and put the tear on the Sheikah symbol. We may never know.

This boss is very similar to both Gohdan from The Wind Waker and Mazaal from The Minish Cap.