If you take too long time in a room...

[Cranky Old Man]

I thought it depended on whether or not you got the vaccine before you got around to draining the sewers, as the shadow seems to appear when it's time to move along.

That isn't the case, because the first time I played through I drained the sewer first and the shadow appeared in the water area, and my friend played this through, and didn't get the shadow and he didn't get the vaccine first either. Pretty sure it depends on your sanity level

Yeah, I checked the code: It doesn't occur if your sanity is above 75 (which should mean "Crystal clear."). My first assumption was wrong.