Jump across the floating dinosaur testicles, or whatever they are, to the grate at the other side. Once you have the pistol, climb up the ladder on the side of the large container. Grab the pistol while the barnacle is occupied, or ride the barnacle up and hit it with your crowbar if you're feeling gratuitously malicious. At least the barnacle didn't digest the guard's pistol.
At the end of this crawlspace is a small room where you'll see a security guard successfully shoot a few headcrabs, but then get grabbed by a barnacle. The platform should lower you to yet another small opening. Turn the wheel labeled 'Flow Control' on the side of the silo all the way, climb the ladder up to the top as quickly as possible, and jump in.
Unless you are skilled at taking out headcrabs without taking damage, avoid them and run straight across the opening to the silo. The tunnel dumps you out into the bright sunshine, surrounded by ponds of goo. Floating pieces of who-knows-what in a vat of delicious green goo.
