Major Sheppard signals to the base that they're coming in fast and arrive amidst enemy fire. They make it through the gate but McKay is hit in the face with a Wraith Stunner and is temporarily paralyzed. The mission is the fifth to encounter the wraith out of nine, raising suspicions that there is a spy somewhere on the base.
Weir calls a meeting, excluding Teyla, and over Sheppard's objections Sgt. Bates, now the head of security, begins to make certain areas of the base off-limits and to interview the Athosians. The Athosians are soon offended by Bates' veiled interrogation and tempers flare. Worse, Teyla is caught in the middle as she sides with the expedition, but isn't happy that Weir is bypassing her.
Meanwhile, working in the Jumper bay, McKay and Zelenka open an outside door. Sheppard and Ford take a flight around, discovering a nearby large land mass. Halling and the other Athosians request permission to live there until they receive full access to Atlantis and depart.
On the next mission, the team is attacked by the Wraith once more and the only remaining suspect is Teyla. She and Ford are trapped as the SG team retreats through the Gate and seal it off. Sheppard insists on rescuing them, particularly when Teyla signals for rescue, and Weir goes ahead and lets them come through.
Bates sends McKay to search Teyla's belongings and he finds the answer: her locket, that Sheppard found in the cave back on Athos, has a low-strength Wraith tracking device that detects Ancients and was inadvertently activated by Sheppard (with the Ancients' gene) when he touched it. Sheppard uses the locket to set a trap and manages to capture one Wraith. As the Athosians and the Earthlings try to set the incident aside, Sheppard threatens the Wraith with starvation until it tells them what they want to know.