Ok, so we know there was a horrible battle in which there was a ton of dead+mangled Russian soldiers. We know the Germans just found them like that and we know that Howard Stark + some unknown general observed the aftermath of that battle. Per Jarvis, Howard got really pissed at the general and built his vault afterwards. We know the government has classified this battle essentially and no one is talking about it. We also know 2 of the supposed casualties were the 2 Leviathan agents, although one of which was apparently rogue. We had assumed Leviathan was after the Captain America blood, but they seem unaware of it and were focused on item #17, which I will call the Event Horizon gas (save yourself from hell!).
So, my guess is that the U.S. (or that general anyways) deployed this gas on the Russians at that "battle". The soldiers basically mangled/mauled each other before (mostly) dying. Stark flies over, sees the results of the gas, and is either a) mortified and decides to nix that shit or b) was not aware they had access to his invention and pissed they abused it. Realizing he can't even trust his own government, he constructs the vault to hide all his WMDs or dangerous inventions. Someone in the US government/military was pissed about this, so they begin to put pressure on Howard. In the meantime, Leviathan had surviving agents from the "battle" and realize that the nerve gas would be a pretty badass weapon, in addition to other Stark inventions. They begin to work their own angle.
IMO, this means that either the US General/government involvement is due to a Hydra/Leviathan plant (unlikely, since the battle was still during the war) or it means simply you have a normal "do whatever it takes to win" mentality and Leviathan employing the same idea in terms of ultimate world domination (ie, Cold War). I'm guessing it will just be a parallel to the nuke: US has the tech 1st, uses it, some folks (scientists) are horrified at how destructive and bad it is, but the military is pretty much "lol we win with this shit!" and is ok with using it, then you have Russia employing spies to steal nuke tech so they can have nuke tech.
