From the introduction:
Hiya, Chuck, it's John.
You probably want to pat yourselves on the back right now. You're all such good little worker Bees, killing the big bad-bad-bad Revenant. But do you understand there's a second story here? Oh, don't you love a good plot twist, Chuck?
You might have noticed there's more than Scarecrows in this two-bit town. The Pathogen is here, too. Not my doing; scout's honour, Chuck. See, the Revenant brought the agents, and then the agents... they brought the Pathogen. They tried to stop it; they wanted to be good little workers, too. They sealed themselves in an exploratory mine shaft outside of town. But their infection, it spread-spread-spread to the groundwater, and that's when things got really interesting here in Blackwood. If you want to finish your mission, that's where you need to be.
Now, I know what you're thinking. “I'm a good little worker Bee. Why should I listen to the big, scary Black Signal?” First of all, I'm hurt, Chuck. Second, well, let's just say there's more at stake here than some dismal little town of backwoods Canucks. You and I, our goals align right now. That's all you need to know for now-now-now.
The tunnel where they sealed themselves is part of a digsite north of here. You can find explosives there to break open the seal. Do it, or don't. Either way, we'll talk again real soon...