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The Stone of Agony is an item seen only in The Legend of Zelda: Ocarina of Time. It is Link's reward from the cursed family for killing twenty Gold Skulltulas. This mysterious rock will shake from within in the presence of secrets, such as the hidden grotto entrances scattered around Hyrule Field. In gameplay terms, this means that if the player had a Rumble Pak or a Tremor Pak inserted into their controller, it will vibrate when Link is near a hidden secret, with the vibration growing stronger the closer he gets. The player will receive the Stone regardless of whether or not they actually have a Rumble Pak.
The following game, The Legend of Zelda: Majora's Mask, has the Rumble Pak vibrate in the presence of secrets by default, though no mention is made in-universe of whether or not this was because Link still possesses the Stone of Agony. Later remakes of Ocarina of Time, such as the Master Quest version, rely on whether or not the player had enabled the vibration feature on their controller to determine the Stone's usefulness. The Stone of Agony is still collectable the game's Virtual Console re-release on the Nintendo Wii, but the Classic Controller has no Rumble feature.
Because the 3DS does not have rumble functionality, the 3DS remake of Ocarina of Time does not support the Stone of Agony in its original form. It has been replaced with a new item called the Shard of Agony. The Shard of Agony serves the same purpose, but instead uses audio-visual cues to alert the player to secrets.