McKay and Weir start repairing the grounding station, while Sheppard tries to fight Kolya. The puddle jumper on the mainland enters the eye of the storm.
Major John Sheppard, Dr Rodney McKay and two other scientists explore a planet where a Wraith spaceship, which crashed there 10,000 years ago, during the Atlantis-Wraith War, is still sending an SOS signal.
It's Elizabeth's birthday and she gets a very special gift: a woman who has been in stasis in an Atlantis' laboratory for 10,000 years and is actually herself.
McKay finds a way to send a message to Earth, leaving space for personal messages. Sheppard and Teyla are off to spy on the Wraith fleet approaching Atlantis.
Teyla is haunted by nightmares, leaving her agitated. After seeing a psychologist, an old Athosian woman tells her a secret about her ability to sense the Wraith.
McKay and Zelenka come up with a plan to repair the Ancients' weapon satellite. Bates and Teyla get into a fight. He is found unconscious and badly injured shortly afterwards.
All hope seems lost, until Colonel Everett arrives suddenly from Earth. He is determined to defend the city until the arrival of a ZPM, brought by a new ship.
The Daedalus arrives and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.
The team discovers a planet where the Stargate is kept on a prison island to keep the Wraith satisfied. Their magistrate is willing to trade a rare mineral.
The team discover an Ancient project to create the ultimate power source. McKay thinks he can finish it. Ronon finds out he is not the only surviving Satedan.
The team find a hidden Wraith girl, cared for by a man with a serum that he claims can satisfy her hunger. Beckett wants to perfect a retrovirus that can turn Wraith into humans.
Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment, stem cells must be retrieved from one of their eggs.