The Two Colonels: After passing the second workbench, you will have to pass through a narrow hallway. Immediately after kicking open the door, look for an opening to your immediate left (a worm will likely crawl out of it). The note will be sitting on a console, along with some flamer fuel.
I hate to say I told you so, but we're screwed now! Cleaning the filters won't help, the pipes are full of slime instead of water now! I tried heating the incoming pipe with a blowtorch some, and the pump did restart after some time, but there's already two fingers of that shit on the walls now, the overflow basin is full, and the only thing that could do the trick is a proper burning! You should have started raising alarm a week ago, and I say that now you should take a brush and clean everything yourself since you were so against the idea of bothering the bosses back then!