The second season focuses on the Atlantis Expedition continuing to make the Wraith think that the city self-destructed, (The Siege Part III) while continuing to explore Pegasus and hunt for ZPMs (although they do have one now) 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 oftentimes 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.