The Ark is the most ambiguous location / aspect of the Marble Hornets series. Something otherworldly, extradimensional, hungry, but definitely associated with the Operator. When characters disappear from footage -- usually after having particularly bad encounters with the Operator or being attacked by Alex -- they are taken to the Ark; the comics have expanded more on how it works, but there is still much left ambiguous. There are ways in and out of the Ark -- Tim and Brian seem to be especially adept at navigating it -- but it is possible to be consumed if one remains inside of it too long.
Archived Material
Eldritch Location: The dark world where Tim ends up in entry #65, implied to be the Operator's domain, seeing how the man Alex killed was in there too (X)
The Reveal: Quite possibly the biggest one in the series comes in Issue 3.5: The Ark is revealed to be an infinitely looping dimension, where the Operator’s victims are stored. (X)