After Sheppard’s return with refugees from Athos, Atlantis, moments away from being crushed, breaks away from the ocean floor, rising to the surface just before the shield fails. Now, given a chance to rescue his people, Sheppard needs to make Weir see things his way.



 

Todd informs Atlantis that a group of Wraith have in their possession several ZPMs which they plan to use to power a new super Wraith Hive. He also advises Woolsey that they should immediately destroy it. But when the team reaches the hive, it does significant damage to the Daedalus and jumps into hyperspace. The team then finds out that the ship is heading to Earth.

 

 

In an alternate reality, detective John Sheppard and FBI Agent Richard Woolsey find themselves in the midst of a CSI like murder case involving several killings apparently of Wraith origin in Las Vegas, Nevada. This episode was filmed in Las Vegas, with filming for the season ending there, but it aired as the 19th episode. During the episode, the songs “The Beautiful People” by Marilyn Manson, “Sympathy for the Devil” by The Rolling Stones and “Solitary Man” by Johnny Cash are played.

 



Dr. Jennifer Keller is diagnosed with a psychological ailment. However, little does the Atlantis expedition realize that she has been exposed to body-switching technology that does not require the subjects to be in close proximity. Meanwhile Keller’s consciousness faces a desperate struggle for survival inside the body of a wanted fugitive woman named Neeva.



 

The team investigates mysterious happenings on board a Wraith Hive. Meanwhile, Dr. Keller is doing research on Wraith physiology.

 

 

Rodney McKay is invited to a landmark scientific presentation by an old rival from his school days. The device appears to be a solution to global warming, but then everything goes awry. Guest Stars include Dave Foley, playing Malcolm Tunney, with Bill Nye and Neil deGrasse Tyson playing themselves.

 

 

John Sheppard has been abducted. After freeing himself from his bonds, he soon discovers who it is who tied him up: Acastus Kolya (Robert Davi). In Atlantis, Woolsey, McKay, and the rest of the team are about to make a shocking discovery about an ancient race called Sakari.

 

 

In search for Teyla’s baby, Michael and his hybrids infiltrate Atlantis. While the hybrids take control of the city’s systems one by one, it is up to Sheppard’s and Lorne’s teams to retake the city. But first McKay has to disable a seemingly inpenetrable stun energy field set up by Michael.

 

 

The Atlantis expedition is put on trial for the crimes against the Pegasus Galaxy by a group of human civilizations that have formed ‘The Coalition’. This episode is a clipshow.

 

 

Sheppard and his team meet a man and a woman named Sefaris and Novo, two of a group of survivors from the planet Balara who survived the Hoffan plague and are now living with the people Dr. Beckett is helping. However, the Balarans face betrayal by their host village when the Wraith come hunting for them.