In the campaign level where you first see the three alien pods, there is a room a few levels under ground. As the story progresses, you end up inside that room, and are told to "get out of there". You then exit, and are confronted by a helicopter.

Every time that I crouch and then jump through the window, (the only way that I know of to get out of that room,) the hud disappears, my weapons disappear, and I can't switch weapons, pull out grenades, etc. Only when I go to am ammo box and hit the use key (F) does the reloading animation play and my weapons are back.