Maj. Sheppard, Lt. Ford, Dr. McKay, and Teyla are in a puddle jumper and they are fleeing from two Wraith dart ships. They are trying to make it to a stargate on the other side of the planet before they are destroyed, as Sheppard is unable to fire back at the darts. They suspect damage was done to their weapons by the darts. Teyla wonders where the short range darts could have come from; was it from a gate, or a Wraith Hive ship?
As things begin to look desperate, a large energy bolt rises from the planet, destroys the darts, and narrowly misses destroying the puddle jumper. Sheppard decides they need to investigate the source of the energy bolt, as it may be powered by a ZPM.
On the planet they find a primitive culture occupying only a small portion of the planet. They are taken to meet the High Priestess Chaya Sar. However, they can’t get any answers to their questions on the weapon, but learn this planet has not been threatened by the Wraith in anyone’s past knowledge. The team begins to see this world as a great possible sanctuary for the people threatened by the Wraith on other worlds. Chaya goes to ask their God, Athar, if others would be allowed sanctuary on the planet. When she returns with the news that no sanctuary would be granted, McKay, believing they are being lied to, gets nasty with his question and pointed accusations. Sheppard, in order to continue the discussions, sends his team back to wait at the puddle jumper.
Sheppard, in hopes of convincing Chaya they are kindred spirits, invites her to visit Atlantis and she accepts. Upon arriving in Atlantis, she gets checked out by Dr. Beckett. Strangely, Beckett finds Chaya’s health is too perfect, unnaturally so. Chaya is then shown around Atlantis by Sheppard, and they even go on a picnic at one point. McKay begins to worry about the closeness developing between Sheppard and Chaya.
During a meeting between Chaya, Weir, Sheppard, Teyla, and McKay, Chaya reveals that she is an Ancient and that she is also Athar. Chaya leaves the meeting but then suddenly feels faint. She feels the Wraith are about to attack her planet and she must leave. She turns into a ghostly cloud and the gate activates, and she leaves. Sheppard says he has to help, and takes a puddle jumper back to the planet. He arrives to see two Hive ships and numerous darts buzzing around the planet. Chaya reappears in the puddle jumper and warns Sheppard to leave, then disappears again. Sheppard leaves just as an energy bolt from the planet devastates all the Wraiths ships in orbit.
Sheppard goes down to the planet and to the temple, to find Chaya. Chaya explains how she is being punished by the other ascended Ancients for breaking their code of not helping corporeal beings. Now she is required to protect the original in habitants of the planet and only those inhabitants, forever. No one else would be protected from the Wraith there. Chaya tells Sheppard her only regret is the feelings she has towards him. She and Sheppard share their bodies together with Chaya in her ascended ghostly form. They glow together.
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