Pretty cool episode, and dare I say it-- the ending was the kind of uplifting, "The universe is an amazing place" kind of ending Star Trek used to do.
At first I found it very, very interesting that we had three plots going on that seemed to have nothing to do with each other. So the fact that they all turned out to be completely connected was great.
Going into it I was a little miffed at their bringing back Kolya. I generally prefer it when characters stay dead. But as it continued and Sheppard's part got bigger and bigger, I found it totally appropriate. Kolya is perhaps the best foil Sheppard's ever had, and their scenes together always work great.
I began to suspect something was up about half way through, but it still kept me guessing as to exactly what-- the device is a prank by Zelinka to finally get back at McCay? Maybe Vanessa was a test put in place by the AOI agent Shen? Maybe Vanessa and/or Shen were Genii plants and Koyle's just keeping Sheppard out of the picture so he can't stop them? But once it was revealed that the Vanessa was an illusion, it all fell into place-- no wonder Zelinka was pushing McCay, no wonder Kolya's back from the dead, no wonder they took such a big step as having Sheppard lose his hand... they were all illusions too. When Vanessa said to Woolsey that she was trying to find out what kind of person he was, I half expected Shen to turn out to be an illusion as well. Normally I might feel cheated at having things turn out not to be real changes after all, but I didn't in this case. The idea that this as an alien race trying to come back from extinction --and needing humanity's help to do it-- was too inspiring for me to feel cheated by everything else.
A very strong episode. As I'd hoped, Atlantis has really come into its own now that it's the only Stargate on the block. It's a shame it only has 5 episodes left.