Sanctuary

Plot
Three Wraith Darts are chasing Sheppard's Puddle Jumper. Suddenly, electricity from the planet below destroys the Darts. Rodney theorizes that there might be an Ancient weapon, powered by a ZPM.

When they land, they find a pre-industrial civilization who know nothing of the Wraith. The people are protected by a being named Athar. The team are taken to meet Athar's priestess, Chaya Sar. Rodney blurts out about the weapon protecting the planet but no one has any idea what he's talking about. Sheppard tells him to be quiet. They ask if refugees can be taken in; Chaya consults Athar and says no. Sheppard invites her to come back to Atlantis, and she agrees.

Chaya undergoes some tests at Atlantis. Sheppard shows her the city and talks about Earth. In the control room, Chaya suddenly activates a bio-detector, and everyone is stunned with the revelation that she has the ATA Gene. Later, in the conference room, they ask Chaya to accept refugees in exchange for advancements in technology for her civilization, but she declines. They then offer knowledge of their religions, which she agrees to review.

Sheppard decides to take Chaya out to a picnic dinner as a show of goodwill. After some talking, they kiss.

Later, Rodney talks with Sheppard and tells him he feels that something is different about Chaya. Carson has found that Chaya is in perfect health, much too perfect for a simple pre-technological society. Rodney is suspicious of Chaya, and concerned that Sheppard is forming such a close bond with her. Chaya overhears him and walks away.

Next morning, Rodney is busy scanning her as Chaya tells everyone that though she is fascinated by their religions, she cannot condone the hate and distrust that the people of Earth display for each other. She points out McKay specifically, especially after his comments of last night. Rodney suddenly realizes that she is an Ancient; she confirms his suspicions, and admits that she did not come to offer her help, but out of a romantic interest in Sheppard.

Before the conversation can go any further, she senses that the Wraith are attacking her planet. She turns into her Ascended form and leaves. Sheppard takes a Jumper and follows her back to Proculus. He takes out a few Darts and Chaya appears beside him and asks him to leave the battle. She turns into her Ascended form again and uses her power to destroy the Wraith forces.

Sheppard comes down to the planet and confronts Chaya. She explains that she is also Athar. Long ago, when the Wraith attacked her planet, she lashed out with one thought and destroyed them all. The Others punished her by restricting her to protecting Proculus only. If she tried anywhere else, she would be stopped. She had been alone for many years until she met Sheppard. After noting that Sheppard will still be permitted to visit her occasionally, she shares herself with him.