“Echoes” is the twelfth episode of the third season of Stargate Atlantis.

Dr. Zelenka, Ronon, and John Sheppard are in a Puddle Jumper returning from an expedition on the mainland to document and hunt local fauna. As they return, Zelenka notices that Atlantis does not appear on the sensors properly. After adjusting their direction by forty degrees they are on the proper course towards Atlantis again.

Teyla Emmagan begins to see repeat visions of Ancients on Atlantis. First she is assumed to be under stress, but after a while other people in the city begin to see the same visions.

A large Flagisallus passes the Puddle Jumper.

Meanwhile, McKay and Sheppard notice a sea creature which Rodney has named “Sam” (after Samantha Carter), because he believes it to be the same one that led Sheppard and Zelenka to rescue McKay from a damaged Jumper on the ocean floor. After using Atlantis’ sensors to find another of the sea creatures, much larger than “Sam”, they decide to take a Puddle Jumper to investigate closer. During a close encounter with the sea creatures, Sheppard and McKay develop intense headaches and McKay falls unconscious.

In the infirmary, Zelenka explains that the sea creatures emit a low frequency pulse and an electromagnetic field which, in combination, are very dangerous to humans. Very soon, most of the city is affected by this. Many victims are transported to the Daedalus, now orbiting the planet, but there are too many in the city to all be relocated.

During his recovery, McKay uses his tablet to locate an Ancient bio-lab dedicated to studying the native marine life and manages to translate what the whales are saying. The Atlantean whales are warning that the sun is about to send out a gigantic coronal mass ejection (similar to a solar flare) straight at the Lantean planet and although the shield will protect Atlantis, the radiation wave will kill all plant and animal life on the planet and destroy the atmosphere, thereby depleting any breathable oxygen. The whales are congregating underneath Atlantis’ shield for protection.

The vision of a Lantean trying to help the burned pilot of the Adaris.

The visions that people have been seeing are a genetic memory that the whales have of this catastrophe, which happens every 15,000 years. The Lanteans were experimenting with communicating with these creatures when this traumatic event occurred. An Ancient ship was near to the sun when the ejection began and most of its crew were killed immediately by the radiation. The pilot managed to jump to hyperspace and overtake the radiation wave before it reached Atlantis and warn the people there.

The Daedalus is hit by the coronal mass ejection.

Now knowing what is happening, the team consult the Ancient database and discover that the last time this happened the Ancients managed to temporarily expand the city’s shield to encompass a large percentage of the planets surface. Unfortunately, with only one functioning ZPM, McKay is only able to expand the shield by a radius of a few kilometers.

In order to save Atlantis as well as the planet, Sheppard comes up with the idea to transfer the ZPM to the Daedalus and move the ship into position between the sun and the planet. When the coronal mass ejection begins, the shields aboard the Daedalus (boosted by the ZPM) successfully deflect the emission away from the planet, with the Daedalus sustaining only minor thermal damage in the attempt.

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