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.

Colonel Sheppard finds himself the prisoner of a Genii commander, along with a desperately hungry Wraith who has been separated from his hive.

The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis's future. The Wraith seek a new alliance with Atlantis in their war with the Replicators.

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

With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.

The team finds their former Wraith ally's hive ship drifting in space, which leads them to a secret project that could turn the tide of a civil war.

"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.