Originally Posted by TheVileOne
Yet the US military is fully aware of SHIELD and is able to associate with them to some degree.
No more so than the way the US military associates with the UN currently; in fact, there's probably less dialogue between the US and the WSC/SHIELD.
I don't recall any scenes in Avengers or *any* Marvel Studios movie that had SHIELD coordinating with US forces. The National Guard and NYPD mobilized, obviously, during the Battle of New York, but clearly they weren't taking orders from SHIELD/Avengers --- NYPD cop to Cap: "Why should I take orders from you?"
And in the battle with Hulk at Culver University in TIH, the US Army engaged the gamma goliath; but the extent of SHIELD involvement was only that Black Widow was "watching over him."