From Halopedia, the Halo wiki
Disappearing Truth is a glitch that can be performed on the Halo 3 Campaign Level, The Covenant. It is a Physics related oddity that sometimes causes the Prophet of Truth's corpse to fall through the ground.
On The Covenant, after you have reached and killed the Prophet of Truth, you can melee (or Teabag) the Prophet once. This will cause him to fall through the platform on which his body rests. Note that the area in which Truth resides afterward sort of resembles a tomb. When he falls beneath the platform, you can see him, though you cannot reach him or get him out again.
Sometimes, the glitch causes Truth's hand to wiggle.
This is a glitch in Halo 3's physics engine, and can be seen throughout the game if enemy or friendly units are killed in certain ways, or are moved to certain places using the melee attack. Another common physics glitch is when units are killed while falling; it causes their bodies to flail about for an extended period of time upon landing.