This poor old thread. But putting aside the dwelling on waiting on more Freeman's mind, I'll give it a shot.
First, let's review:
The crazy guy didn't start off insane. This gent investigated a sound in the tunnels and lost it (and is now trapping others???)
Dave is speaking gibberish, but a bit of it is recognizable. "Ba Weep Grana Weep Ninibong," is a universal alien greeting. Someone else is welcome to translate the rest. He also won't use his flashlight (wouldn't be surprised if that had to do with something.)
Mike and Dave have noted that everyone seemed to have disappeared.
The tunnel seemed to have recent construction work.
Okay. My take on it:
The noise is made by the Nihilanth's successor or some last remnant. It could float through the tunnels and teleport its victims, like Dave, into that alien cocoon. Then, it's aim is to mutate or modify the person into some kind of remote control human to open a portal between Earth and Xen. Now that it has the English gent's mind under control, it's attacking Civil Protection to get closer to those in charge and eventually seek out revenge on both Freeman, Earth, and / or the G-man.
The stilt, body-junkie guy, (how about 'Stilts') was also frightened by the noise. I think he was a previous victim, an earlier experiment. And I think he was honestly trying to help Mike with his stilt-stub-arm probing.
The little monsters could have bitten Mike's head off in that split-second, but you hear Mike rant during the credits. So those things aren't the real enemy. Perhaps they're scavengers, not going for the kill, but the encasement of alien meat surrounding Mike. Dave is still talking, so maybe he will eventually communicate to the monsters to cut them loose. But it could also mean the unseen culprit has hacked into his mind.
So what about the car? Remember no-shadow guy? Keep in mind that he ran off into the tunnel.
This is all leading up to the Nihilanth's progeny's attempt to invade Earth from Xen by using human puppets to open a portal. And since it involves using mind-power, it could all come from Dave, (who wanted that super power if you recall.)
This is going to take place in... wait for it... ... ... Dave's Mind. Episode One. Where he saves the day by closing the portal ninja-style and with the help of his recruited alien friend, the freaky bug-eyed dog thing.
Meanwhile, Mike has gotten loose and has teamed up with Stilts to get out of the tunnel (Dave is on Xen at this point.) Mike finds a convenient crowbar and Stilt's arm-probes help to pry open the door. Crazy Gent isn't there. And surprise! No-shadow guy rushes past them into the tunnels. Having driven recklessly out with the car, he returned with a whole mess of CP back-up. Everyone runs into the back tunnels- way back- into the huge chamber where Dave has successfully reemerged with the new Nihilanth and closed the portal. CP soldiers shoot many glorious bullets and they take that thing out once and for all. Mike and Dave high-five. CP decides to reconstruct the tunnels into the biggest donut shop ever. Stilts gets a job as a donut chef and he's pretty good at it. All seems well. The last part can show No-shadow riding a train. you can see he's not making a reflection in the window either. He arrives at the old apartment where Crazy Gent has returned. Crazy Gent is still crazy. And No-shadow vampire guy sneaks up aaaaaaand- cut!
That's what you get Crazy Gent! For being scarier at the very end of the video than at any other part!