Despite my reaction to the season premiere, I'm not sure I was ever convinced that Michael was dead. I think it was more a reaction to the notion that he was being treated as dead again; I liked him better as an active villain. This episode demonstrates why Michael is such a potent adversary, especially in the wake of the previous episode.
One item that Team Atlantis could not defend themselves against during the Coalition "trial" was Michael's creation and subsequent reign of terror. Michael never would have existed without the ill-advised experiments on Atlantis, after all, and while it's hard to say that they dropped the ball on taking Michael down given their efforts, they bear some responsibility for his subsequent actions.
Michael manages to take over Atlantis (as so many others have) for the purpose of abducting Teyla's child so he can continue his work. The plot doesn't get much more complicated than that. Sheppard and McKay work to find a way to counter Michael's control of Atlantis' systems, Ronon attempts a more straightforward counterattack, and Teyla desperately tries to keep her conveniently quiet child out of Michael's clutches.
In other words, the story is quite predictable. There's even a moment where Teyla tries to hide from Michael, scrambles into the functional equivalent of a closet, and the baby makes the requisite cooing noises. And of course, it's the only time the baby makes those noises in the entire episode! It couldn't be more of a cliche, and that's the problem with 90% of the episode.
Thankfully, there are some shining moments. Michael wants Teyla to understand his motivations, but he has serious drawbacks in his moral justifications. It's fascinating to watch him struggle with the notion that Teyla doesn't see that he's the victim, and that he's doing the right thing. And of course, he fails at every chance to show true compassion or mercy, which simply underscores the threat that he has become.
Which makes it that much better for Teyla to make the decision that Michael must die. Michael spoke to the fact that Teyla had been the most compassionate member of the team during his time with them, and it comes full circle when she makes the choice to kill him. It's played as the brutal choice of a mother protecting her son, but this calls back to her initial role as the "warrior queen". Teyla doesn't wear the stylish leather bustiers for nothing.
So, surprisingly, the character aspects of the episode made up for the lack in the plot. I'm not sure Michael is dead this time either (he is resilient, after all), but if he is, perhaps it's for the best if he is. With the end of the series swiftly approaching, there's nothing wrong with tying up the loose ends. And, as Teyla mentioned in the episode, without Michael, there's always someone else waiting in the wings.