A hive ship comes out of hyperspace directly over the city of Atlantis and transmit's a garbled message. Despite missing data, McKay is able to make out a reference to Dr. Keller's gene therapy and an urgent request for help. On high alert, Col. Sheppard and his team launch a cloaked puddle jumper to investigate. They board the ship to discover the entire crew in stasis, and a prerecorded message from their nemesis Todd.
In it he reveals that he and the crew were stricken with a disease - a complication of the gene therapy developed by Dr. Keller, which they had tried to self-administer. Many died and the rest were put in stasis. Now, they need Atlantis's help.
After much deliberation, Mr. Woolsey gives his approval. Back on the hive ship Dr. Keller struggles with the complexities of Wraith physiology as the other team members begin to notice something very unsettling - the hive ship itself has somehow been impacted by the disease, with dire consequences for all on board.