Rodney McKay awakens in his lab, tied to a chair and with no memory of who or where he is. He did seemingly leave himself a video message telling him to look for Teyla. The problem began some 14 hours before when Dr. Katie Brown returned to Atlantis with plants from a planet she had visited. The plants had been cleared through the normal quarantine procedure but she is soon afflicted with severe headaches and loss of memory, eventually falling into a coma. Memory loss begins to afflict other members of the crew but they soon become distrustful of one another, making conclusions based on false assumptions and a misreading of the situation. Fortunately, there are two members of the team who seem to be immune.

The Atlantis team decides to attack the numerous ships of the Replicators, with the help of uneasy alliances.