he second season of the television series Stargate Atlantis commenced airing on the Sci Fi Channel in the United States on July 15, 2005, concluded on The Movie Network in Canada on January 30, 2006, and contained 20 episodes. The show itself is a spin off of its sister show, Stargate SG-1. The series was developed by Brad Wright and Robert C. Cooper, who also served as executive producers. Season two regular cast members include Joe Flanigan, Torri Higginson, Jason Momoa, Rachel Luttrell, Paul McGillion, and David Hewlett as Dr. Rodney McKay. The second season focuses on the Atlantis Expedition continuing to make the Wraith think that they self-destructed the city while continuing to explore Pegasus and hunt for ZPMs this means at times lying to new allies about the city even sometimes claiming to be a small contingent that escaped the Siege; the season also marks the first time the Expedition is able to make contact with Earth although doing so uses a lot of power so the contact is at often times via the Daedalus, an intergalactic Earth-Asgard vessel commanded by Col. Steven Caldwell who makes clear his desire to be Military Leader of Atlantis but eventually settles for a sort of advisory role as it becomes clear that Dr. Weir and the Lt.Col Sheppard are a duo not to be messed with. The central plot of the second season is the development of Dr. Beckett's retrovirus, which can, theoretically, turn a Wraith into a human.

Overview from themoviedb.org