The first episode "Condemned" the Atlantis team finds a culture that lives in relative safety from the Wraith and the team later on find themselves strandard on a penal colony after being shot down by the inmates. The episode deals with some moral dilemma issues for Sheppard in particular, the SFX are again pretty good.
"Trinity" is an ok episode, it mainly follows Dr.McKay and his team of scientists trying to get an Ancient Weapons Platform working. The episode focuses on McKay and how arrogant he is and also how smart he thinks he is, which backfires later on.
The sub-plot of Teyla and Ronan adds nothing to the plot line, but allows the two characters to develop more.
"Instinct" is one of my favourite episodes this season. In this episode the team travel to a world that is under attack by a creature which sounds like a Wraith. However the team find Ella, a young female Wraith bought up by a human. He claims Ella is not like the other Wraith, but we soon learn that she is not all that she seems.
"Conversion" follows on from "Instinct". Sheppard starts to change into the iratus bug and the team have to race against the clock to save him. Any suspense in this episode is blown out of the window straight away, as it's obvious that Sheppard will recover b4 the episode ends.
Hopefully all these episodes will have audio commentaries, and also a few special features on the making on these episodes.