The writing for the good guys and their acting are all relatively weak this episode, although I thought Paul Herlinger did a pretty good job in the climax.
There are a lot of cheesy things and weaknesses in the plot (the big one being, as someone pointed out in a post years back, that the analogy they're driving at falls flat because Whit didn't personally sacrifice anything), but one other part where I think they drop the ball at the end is when Connie asks something like "Is Blackgaard truly dead now". I think Whit commented on this earlier in the episode, but it was forgotten by the end: the real Dr. Blackgaard died years ago, at the time this episode is portraying. The virus might have something like his personality or memories but his soul is long gone.
That said, whenever Earl Boen is "on screen", the episode magically becomes interesting. I remember being appropriately scared when I was a kid listening to the Civil War scene at the beginning, and I think he did a good job in the climax as well.
Some people look at it as a lowlight in Odyssey history. They have some good points, but I'd urge them to look at the bright side -- they could have brought Blackgaard back to life and made DBD completely pointless. Instead of that, we got this. It's a very flawed two-parter but I think it's enjoyable if you make the effort.