Having tricked the humans of Atlantis into revealing the location of Earth, the two Wraith hive ships immediately set course for this rich new feeding ground, carrying Dr. McKay and Ronon with them as prisoners. Although they don't know it, they've also got a third human passenger: John Sheppard has managed to piggyback his small F-302 fighter onto the underbelly of the first hive ship.
Back in Atlantis, Dr. Weir realizes that just one chance remains to stop the Wraith from reaching Earth. After the first stage of their intergalactic journey, the two hive ships will have to drop out of hyperspace briefly at a desolate site just outside the Pegasus galaxy. Weir orders Col. Caldwell to lead the Daedalus and the ancient Atlantean warship Orion to a dangerous deep-space ambush at that location.
At this critical moment, three ambassadors from the International Oversight Advisory demand that Weir return to Earth through the stargate to meet them in person. Once she arrives, their bureaucratic dithering almost delays Caldwell's mission, but Weir stands strong. Soon Caldwell's small fleet is underway.
As the Wraith ships drop out of hyperspace, Sheppard seizes his chance to do some damage before he's captured or killed. He manages to blow up one hive ship's ventral hyperdrive generators. Then he's seized by a swarm of Wraith. His salvation comes from an unexpected source: Michael, who has been rejected by his fellow Wraith for being contaminated by humanity, decides to free Sheppard and help him rescue McKay and Ronon.
As the two make their way toward the cocoons where McKay and Ronon are imprisoned, the Daedalus and the Orion arrive with guns blazing. The Orion obliterates the second hive ship with a barrage of Atlantean drone weapons. But the time-ravaged Ancient warship can't last long in the fight. With its systems failing, its crew beams to the Daedalus for safety.
Sheppard and Michael find the cocoons empty - Ronon and McKay have already escaped. Sheppard guesses that they'll head for the nearest control station to sabotage the ship. Sure enough, McKay and Ronon are doing just that. Reunited, the four escape to the Daedalus aboard a transport craft.
Alas, the badly damaged Daedalus is hardly a reliable lifeboat. Even if it survives the next Wraith assault, its life-support systems are already beyond repair. Stranded in deep space and outnumbered by the enemy, the crew must now also face the imminent threat of asphyxiation.