The Ark is a location, object, person, or group that is referenced multiple times throughout several ARGs relating to the Slender Man Mythos. The actual existence of The Ark is unsure, as to what it is, why it is there, and how it has come to be are uncertain. Why it is of great importance to The Operator isn't certain either, nor is how to find it or what it is capable of.
Due to the very limited nature of The Ark, little can be factually stated beyond concepts and assumptions.
Marble Hornets internet stalker Totheark
Totheark is the only person in the Marble Hornets ARG that appears to be involved with The Ark. He or she never directly states what it is, where it is, but the audio in several of the videos seems to imply they want Jay to lead them to it. As stated in the Marble Hornets Wiki page, the person, group or even entity behind the YouTube channel hasn't been revealed yet. Based on recent footage it is speculated that Totheark is Hoody.
A potential theory is that "The Ark" is some form of acronym for a name, however who it would be is entirely debatable.
A relatively popular theory that Alex is "The Ark," followed the acronym theory: Alex R. Kralie. However, this theory has been proven wrong by Jay, stating Alex's middle name doesn't start with an 'R'. Furthermore, in Entry #79, Jay finds a note saying: BENEDICT HALL: FIND ALEX AND THE ARK, stating that Alex and the Ark are separate beings.
Other Theories include The Ark being a place where one is safe from The Operator, a repository of knowledge (similar the ark of the covenant), particularly knowledge concerning the Operator and possibly how to escape him or defeat him, or one of the two "Ark"s from The Old Testament, Noah's Ark or The Ark of the Covenant (or at least takes its name from/or is related to them).
Another proposed theory is that The Operator may be actively trying to kill itself by means of damnatio memoriae. If this is true, it may be actively manipulating Alex and using The Ark as some sort of burial ground for any information connected to it. This would allow it to hide the bodies of any victims or store objects of significant importance away from any human beings. This theory, however, only works if one assumes Alex is being misled by his own grandeur in attempting to kill The Operator and unknowingly helping it, or if Alex and The Operator have the same goal of killing The Operator himself.
In the end, however, The Ark was never directly stated to be found. Tim and Jay never show themselves finding it and thus it appears it will remain uncertain exactly what The Ark is.
There is a video that isn't a part of the official video list on YouTube that features Vincent, Evan, and Jeff in the basement of Evan's house, where it is totally dark. Everyone seems to be injured with medical tape on their wounds and heavily on edge. Jeff notes that they haven't seen anyone in what they assume to be days. Electricity seems to be not working, the sun hasn't been out, according to Vincent, in "Three Days" while Jeff feels it has been "an hour". They mention having been in the company of a doctor (most likely Doctor Corenthal) but he has gone missing. They are then attacked by The Rake in the basement, and try to flee, but just as Jeff gets taken the video cuts out. The events shown in the video are never brought up again, making its placement in the EverymanHYBRID canon questionable. However, the opening moments of "Welcome to the Ark" were used again in the final moments of "Twenty-four months," which may further insinuate its canonicity.
Between the two videos, EverymanHYBRID has given more information, but due to the nature of Marble Hornets staying away from involvement with other ARG's, it may be different there. EverymanHYBRID seems to show that The Ark is a totally different dimension where time passage is off, clocks don't work, electrical equipment that doesn't have batteries has failed, water causes harm to humans, there are no people, and it can be assumed the Rake has full and complete access to it. Due to this video being a video randomly posted outside of the EverymanHYBRID videos it can be either considered from the future or non-canon, however how the footage could have gotten recovered from The Ark isn't explained. One theory that could also coincide with the video is that it isn't our EverymanHYBRID crew, but another crew from another universe.
In Tribe Twelve's video "Bridge To Nowhere", Noah Maxwell is transported into the Ark, where he is stalked by HABIT from a distance. This seems to imply that the Ark is HABIT's domain, which is supported by his statements : "Yeah, let's run from him in his own house", and "I don't remember letting you in."