At the end of season 2 of Stargate Atlantis, Atlantis had made a deal with some Wraith and the deal had gone bad. As usual so far Sheppard is believed dead. Ronon and McKay are in danger. This is what the first two episodes of Season 3 resolve. Both seasons are now available as part of the 26 DVD Stargate Atlantis The Complete Series set. Season 3 features 20 episodes on 5 DVD.
The Stargate people are not the usual kind and always compassionate humans usually depicted in SF TV series. These characters have a dark and mean streak. The season deals with biological warfare and its aftermath. Later, they are no above destroying an entire race to save themselves, again.
An especially good episode is McCabe and Mrs. Miller where Rodney and his just as brilliant sister work together on a physics thing. The Tao of Rodney where he gets superpowers and a crisis of faith is just as much fun.
Richard Kind (Spin City) has the time of his life as an irresistible being in a couple of episodes. Even the Stargate Atlantis people have a hard time resisting him. Kind is good but the episodes pointless. David Ogden Stiers (MASH) plays the leader of a group of Ancients who do not take kindly to the Atlantis people.
Season 3 introduces a couple of new villains.
The whole tell Rodney he can't do something so he will do it gets quite tiring by the time it is overused in Stargate Atlantis season 3. The season ends in a "the end is nigh" cliffhanger, again.
Stargate Atlantis Season 3 features two Star Trek alumni. Robert Picardo (the doctor on Voyager) gets a recurring role. Connor Trinneer, Trip on Enterprise, plays a Wraith named Michael.