As Sheppard's team helps Weir and a bevy of scientists explore an Ancient drilling platform on the ocean floor below Atlantis, Teyla warns the group that she senses a Wraith nearby. To confirm that she's correct, she tries to make direct psychic contact with the Wraith. Surprisingly, she emerges from her trance declaring that she was mistaken, so the relieved team resumes work.
The moment that Teyla's alone with Ronon, however, she attacks him. Leaving him unconscious, she sabotages the platform's critical systems. Then, just as Sheppard and a groggy Ronon corner her, Teyla reverts to her normal self. It turns out that a Wraith queen, hiding nearby, has been possessing her mind ever since their initial psychic contact.
The Queen sneaks through the disabled drilling platform, feeds upon one scientist, and then she uses another to lure Sheppard to the team's Puddle Jumper. With her formidable psychic powers, she almost coerces Sheppard to fly her to the surface in the Jumper before Ronon intervenes. Ronon stuns the queen long enough to capture her, but he also accidentally shoots out the Jumper's front window, flooding the craft. Now the team is trapped on the drilling platform.
Although bound and sedated, the Wraith queen smugly announces that her captors will soon die. Teyla summons all her strength and enters the queen's mind to pry loose more specific information. The psychic interrogation is exhausting and carries a constant risk that the queen will regain control of her, but Teyla learns that thousands of years ago the queen's cruiser crashed into the ocean during an attack on Atlantis. Trapped on her ship, she survived by hibernating and feeding upon her crew until only she remained. When she sensed Teyla's presence, she hungrily swam from the wrecked cruiser to the nearby drilling platform.
Worse, Teyla discovers that before the queen left her cruiser, she programmed it to self-destruct. The imminent explosion will shatter the unusually thin planetary crust in this area, triggering a volcanic cataclysm that will destroy not only the drilling platform, but also Atlantis far above.
Sheppard and McKay quickly don 10,000-year-old diving suits and make a dangerous transit from the platform to the queen's cruiser. There, they discover that only the queen's secret command code can stop the self-destruct sequence. Teyla must push the limits of her psychic endurance and enter the Wraith's mind once more to get the code - but this time, the queen is ready for her.