Colonel Carter attempts to lead a rescue mission to save several trapped Atlantis team members, unaware that Michael is closing in on their position with a heavy cruiser.

After Dr. Keller removes Beckett from stasis, she gets infected with a dangerous entity that begins taking over Atlantis.

Ronon is captured by his former friend Tyre, who plans to turn him over to the Wraith to get back in their good graces.

Sheppard's team finds the Earth ship Daedalus abandoned and without power.

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. Barely able to return to Atlantis, the Jumper seems to infect the city's systems with what seems to be a computer virus.

McKay begins to lose his memory after contracting the Pegasus version of Alzheimer's called "Second Childhood."

Sheppard and Beckett are terrorized by deadly creatures on a planet housing one of Michael's research facilities.

Sheppard's team accompanies Todd the Wraith on a mission to negotiate an alliance with another Hive with Teyla playing a key role when she's surgically altered to be a Wraith Queen.

Keller is abducted on a trip off world to help a wraith-threatened village, and it's up to Ronon and McKay to find her. However it soon emerges that her abductor is, in fact, a Runner.

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.

McKay returns to Earth to witness the unveiling of his rival's latest breakthrough.

Sheppard and Lorne investigate a Wraith Hive Ship that has been infected with a strange disease.

Dr. Keller's body is taken over by a cunning thief, who uses the situation to try and acquire advanced technology from Atlantis.

In the city of Las Vegas, Detective John Sheppard must solve the case of a long string of unusual cuddles.

Todd brings Atlantis news that one of his underlings has obtained a ZPM, and plans to use it to build a new Hive supership... and attack Earth.