Apparently most of the people that are trying to break this myth haven't been paying attention to two important game entities, one is a radio and the other - a character. The first connections were made to the 'epsilon cult', which would've made sense if the building's name wasn't "research lab" (from mta). As the wiki says, 'despite it's grand nature' it's not a part of the main story and the players, naturally, started being suspicious of it. But what is it really?
What is it? It looks like an abandoned supermarket and that's pretty much the only thing we can instantly rule out - as the town closest to it has less than 250 citizens; and the road that connects them isn't even paved.
Looking back on the missions with the Truth - if you remember 'The black project', he drives you down to A69 and kicks you out of the car to do the mission on your own. In 'Green Goo' he goes on to do absolutely the same; yet if you listen to WCTR, he confesses to the radio host that he'd "been inside, inside everything, seen everything. Remember the first time you did mushrooms? There are aliens living in the state, aliens,
and I held them in my own hand! Everybody, go to the desert, beg their forgiveness!". Upon being asked how does he know that, he answers that he had been to their 'camp'. Area 69 is notable for the alien-affiliated activities within, but he never entered it. As he is a junkie, he'd probably pick a secluded and empty place to do his drug, and what better than a building that seems abandoned.
So he probably broke in to discover more than he expected - perhaps an experiment went wrong, or perhaps the aliens were forced to land on Earth, find a place they know and hide there.
In the game, Truth and Toreno are two sides to the same coin - they work and profit from the government, both are rather secretive ("He's like the devil" -CJ, Black Project) and speak on need-to-know basis only. And when Toreno says "we're the fucking pivot", he probably doesn't get the fact that he's on one side of the scale of something too. Truth however appears to understand how the scales of life get their imbalances ("Everything is transient" - Truth, Black Project); as he asks the player "Do you know what you're doing for Toreno?" it should be clear to the player that the hippie is well informed on Toreno's actions. Continuing the dialogue, Truth says a few things that are also weird: "[...] No more. We're not alone! [...] A place, that isn't on the map...[...] A train is about to leave". Following this chat, we can figure out that the Truth is talking about the two consequential missions from the airfield; and he probably didn't read the information he possesses, but instead overheard it in a discussion. And the mushroom remark weighs in; as people perceive objects/beings quite differently on psy-drugs, perhaps he was scared shitless, like many people that do those 'for the first time'.
So my point is that this abandoned building is a research laboratory which was probably abandoned due to amortization and lack of space; probably everything was moved to A69, was empty for some time and is now an alien 'camp', which the Truth has visited and gained the missions from the unknown beings that occupy it. And perhaps the green goo itself was stolen from them in the past and they were giving the Truth different ways to get it back, without it looking too suspicious - imagine an alien trying to sneak in a base, built to keep aliens inside (as the real myth goes) or visiting an urban train station to try and snatch some military cargo.
-by SilverFletcher