There were many plot holes (not killing or at least securing Ronin, and many other things), but those are things I can ignore and still enjoy the story. But there is one thing in this episode, that I find very disappointing. Atlantis didn't have to pay a high enough price for their actions!
So what do I mean by this? The team of Atlantis did several things, which were at least morally questionable:
- They captured Michael (morally ok, since they are at war) and used him to test a biological weapon (morally definitely not ok)
- After helping them to defeat two hives, protecting Earth and getting their ship AND the conquered hive back to Atlantis, they thanked him by transforming him AGAIN, even though he would have preferred to be killed! (I would call this kind of behavior not only morally wrong but downright "evil")
Yes, Michael had to be stopped. He was evil and a great danger to many, many people. But it was Atlantis who's (morally wrong) behavior created this threat in the first place and for that they should have had to pay the price! Killing Michael should have cost some terrible price (one or more main charakters get killed or permanently maimed, Atlantis suffers permanent damage, or something like that ...)
The reason for this is simple:
In a universe like "Star Gate", where in the end good always prevails over evil, evil deeds should never go unpunished! Especially if the "good guys" are the ones commiting those deeds!