When an operative of the Trust plants a bomb in Atlantis, the team must find a spy within their own ranks before the Wraith arrive and discover the city.

The team desperately attempts to stop two Wraith hive ships from reaching Earth. Sheppard must rely on an old foe to rescue McKay and Ronon.

The Atlantis team must decide the fate of a colony of Wraith they have turned into humans. Dr. Weir must defend her leadership when she is evaluated by the I.O.A.

Rodney McKay goes in search of his sister on Earth after she is kidnapped by the head of a powerful corporation.

Teal'c visits Atlantis to counsel a headstrong Ronon, who is up for review by the I.O.A. But the two must work together when the Wraith invade the Midway space station in order to reach Earth.

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.

In the city of Las Vegas in an alternate reality, police Detective John Sheppard investigates a series of bizarre murders where each body appears to have desiccated. He is soon called to Area 51, where Dr. Rodney McKay explains the situation.

"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.