After a brief conflict with Michael, Colonel Carter attempts to lead a rescue mission to save several trapped Atlantis team members.
The team removes Beckett from stasis to help out in a dangerous situation.
Ronon is captured by his former friend Tyre, who plans to turn him over to the Wraith to get back in their good graces.
A malfunction in the Daedalus results in the team meeting different alien life forms and having to battle.
When Sheppard and his team are about to return from an off-world mission with their Puddle Jumper, the systems of the Jumper go crazy.
McKay begins to lose his memory after contracting the Pegasus version of Alzheimer's called "Second Childhood."
While exploring an abandoned catacomb on an unexplored planet, a team discovers one of Michael's secret labs.
Teyla goes undercover on a mission aboard a wraith hive ship.
Ronan must use his skills as a former runner in order to save a kidnapped Dr. Keller.
Daniel Jackson visits Atlantis to do some research on the Ancient scientist Janus.
Sheppard must rescue McKay and Daniel Jackson from an Ancient laboratory that belonged to Janus before Todd, who has hijacked the Daedalus, gets there first.
When the Wraith discover that a small group of survivors of Michael's release of the modified Hoffan drug are hiding among the population of a village on another planet, Sheppard and his team must convince the entire village to evacuate before a Hive Ship arrives.
When Sheppard and his team are brought to trial by a Coalition of human worlds for what they claim are crimes against the people of the galaxy, it's up to Woolsey's legal expertise to clear their names.
Michael besieges Atlantis in an attempt to kidnap Teyla's infant child.
While exploring the mainland of Atlantis' planet, Sheppard is captured by a foe believed to be long dead. Meanwhile, Woolsey's job is at risk and he has an important decision to make and McKay and Zelenka make an interesting undersea discovery.