For a mid-season finale, there are very few location shots in this episode.
We get a wider shot of the warehouse where Barnabus' STO cell operates:
This pretty well cements my hunch that this is an entirely CG location.
We then visit a lake in V-world:
Per the good folks at MovieMaps.org, this was shot at Sasamat Lake near Coquitlam (here's an aerial):
Finally, an actual location to find! Vergis and Col. Patel leave a building in the dark & rain:
The staircase is at Oceanic Plaza - the railing and surrounding concrete structures are very distinctive, not to mention the fountain in the upper-left side:
The building across the street is Guinness Tower:
I had hoped that the lit sign from the screen capture would lead me to this building, but I couldn't resolve it properly no matter how much I played with the image. Fortunately, it wasn't a problem.
Was it luck that I found this quickly and with so few visual clues? Or, am I finally getting inside the mind of a Vancouver location scout? And if the latter is true, I am available, TV & movie producers ;)
Later, Amanda thinks dark thoughts:
...and sees a bridge...
The bridge is the Burrard Bridge, and given Amanda's relative position, I believe the path she's walking on above is near the Vancouver Aquatic Centre (the oddly-shaped building on the bottom-left in the picture below):
And here is a picture I took of the bridge in the summer of 2012:
What an exciting mid-season finale! See you in 6 months for Episode 10. (Just kidding!)