A week after the battle with the Replicators, the Atlantis team spots a Wraith hive ship adrift in space. It belongs to the particular Wraith who was first a captive and later an ally of the team, whom, for convenience, Sheppard now calls "Todd".
Curious about Todd's fate, Sheppard's and Lorne's teams board the battle-scared hive, which is empty except for a few corpses. After McKay and Ronon discover a map to a mysterious planet that the Wraith seem to consider sacred, Teyla - whose Wraith DNA makes her the only person who can control the ship - flies the hive to this new destination.
Sheppard, reluctant to let Teyla take risks now that he knows about her pregnancy, orders her to remain in the hive ship with Lorne's team while he, McKay and Ronon fly down to the planet in a Jumper.
Sneaking into a vast facility on the surface, they find a Queen Wraith fertilizing pods that grow new Wraith drones. Tens of thousands of empty pods fill the eerie structure. Enemy Wraith patrol the corridors, and soon the team finds Todd himself locked in a cell.
When the teams free Todd, he explains that this place is a unique cloning facility, where a Queen's moderate output can be copied many times over to breed a vast army. It hasn't been used in generations because it requires multiple ZPMs for power. Todd, hoping to clone an army for himself, stole several ZPMs from the Replicator city seconds before it was destroyed, but other Wraith learned of his plan, attacked him, and took the ZPMs.
Now, Sheppard's team and Todd once again have a common purpose: to remove the ZPMs powering the facility so that Todd's (and Atlantis's) enemy can't create a massive army.
No sooner have they agreed to collaborate than the enemy Wraith spot them. Todd escapes, but Sheppard, McKay and Ronon are dragged before the Wraith Queen as prisoners. Just as the Queen prepares to feast on McKay, however, she hesitates.
Moments later, she speaks to the team as if she is not the Queen at all, but rather Teyla. In fact, Todd has stolen a dart, flown to the hive ship, and alerted Teyla to the crisis. With her psychic powers augmented by her pregnancy, Teyla has taken control of the Queen's body.
Teyla forces the Queen to release the prisoners, but the alien woman remains a formidable foe. Locked in a psychic battle with Teyla, the Queen reaches out to destroy that which Teyla holds most dear - her unborn child....