"Todd" informs the Atlantis expedition that a rogue group of Wraith has acquired several Zero Point Modules to power a Super-hive, and wants it destroyed. However, after the Daedalus is disabled, they learn that the ship is heading straight for Earth, and they must stop it before it gets there.
After a Wraith Hive Ship shows up over Atlantis transmitting a distress call, Lt. Colonel John Sheppard's team discovers that its crew has been stricken with a disease they helped create.
Dr. Rodney McKay reluctantly returns to Earth to witness the triumph of his rival Dr. Malcolm Tunney, but must help shut down a deadly weather device when the new technology goes horribly awry.
While on a mission, Lt. Colonel John Sheppard's team inadvertently brings a mysterious entity to Atlantis. They soon learn that the entity is nothing more than Dr. Elizabeth Weir, who was thought to have been killed after her capture by the Asurans.
Lt. Colonel John Sheppard and his team are trapped under the rubble of Michael's facility in order to rescue Teyla Emmagan. As Colonel Samantha Carter launches a team to rescue the rescuers, little do they know that Michael Kenmore is also searching the planet for the survivors.
With the Ancients' city of Atlantis discovered in the Pegasus Galaxy by Stargate Command, Dr. Elizabeth Weir and Major Sheppard lead a scientific expedition to the ancient abandoned city. Once there, the team not only find themselves unable to contact Earth, but their explorations unexpectedly reawaken the Ancients' deadly enemies, The Wraith, who hunger for this new prey. Now with the help of newfound local allies like Teyla Emmagan, the Atlantis Team sets about to uncover their new home's secrets even as their war of survival against the Wraith begins.