Hi again, it's me, I know, i know, your probably all saying "Vinnie, this thread has been dead for almost a year now, what are you doing here?" I just had a thought and i would like to share it as a theory ,or if the story isn't done yet, idea for how it would turn out and how everything from the episode links together. My guess is that a mad scientist who formerly worked at black mesa in "questionable ethics" wanted to find a way to control the headcrab zombies and have them invade the city without killing any of the citizens. but to do so, he had to extract a pheromone from the headcrabs as well as a fluid the headcrabs have to use to take control of the host's brain. He got a green light from the rebel commanders to go ahead with his research. Him and his assistant were looking for a place to set up, when they found a door inside the tunnel. At first glance, it looked like a construction project, but as they head deeper inside, they found the "dug-out" tunnels, and after following the tunnels, they managed to find an elevator that leads down to a secret laboratory that was used by Aperature science in the 1970s (when i took a look at the maps in hammer, i noticed that behind the corpse where Dave went missing, there was what looked like an elevator) They found that it was the perfect place to study. After a few months of research, the doctor started to get a god complex. He discovered that he can use the headcrab's cerebral fluids to create an airborne disease, without having an individual headcrab on a host. His assistant took note of this and tried to stop him. He anonymously contacted the Overwatch and disclosed the lab's location. The entrance to the construction site was blocked so the overwatch team had to breach it with explosives (the hole in the wall). The soldiers came in and hiked through the tunnels and found the elevator where they came down to the lab and took the doctor for questioning. The overwatch intelligence saw this as an opportunity. They didn't have to stuff feral headcrabs into the canisters anymore. They could just gas the rebel bases with the virus inside the shell. After testing the virus on human test subjects, They started to mutate into zombies, only this time they were enhanced in many ways, first having predatory intelligence, making them masters at hiding in the dark and striking at their prey in the most gruesome and effective ways. Also their appearance is altered drastically from regular zombies, giving them enhanced muscle and bone structure making them hard to kill when confronted with a regular body shot. Most of all, they don't need headcrabs. They also have the old zombie infection technique. Biting will infect. They had at least 100 test subjects in the labs. The doctor broke his deal with the combine by releasing the zombies from stasis. The overwatch were overwhelmed and fled to the elevator, which as a fail safe, the shaft was rigged with C4. The doctor also boarded up the entrance so they could not dig down either. He thought the zombies were trapped for good, but being the masters of stealth, several managed to climb up the elevator shaft and escape without anyone noticing. The doctor was killed as the soldiers ran out. (the body we saw in front of the elevator) It was only 5 years later when the diary owner came across the tunnel and found the zombies, he never found the lab though. But he possibly found the doctor's body, hence the scream from inside the tunnels. The slugs though were possibly the FAILED experiments on animals, or even other xen creatures.
EDIT: To explain the insanity of dave and the diary guy. Maybe the bites of the zombies create dementia within the brain before the final mutation. To fully infect the host, the virus is going to have to get into the brain, just like the headcrabs did. this can easily and simply be done by biting one of the jugular veins which resides in the neck and the forearm. Almost all veins in your body have to reach the brain to provide it with blood. Not having enough blood inside your brain will lead to a stroke. Biting the jugular veins will quickly infect the host by spreading the virus throughout the body's veins and the heart.
Well, that's it, sounds pretty legit. I wish this would actually make it onto the episode, seems like a legit story line.
