Terrifying nightmares about the Wraith cause Teyla to lash out at her colleagues and prompt her to seek professional advice. With psychological guidance, she discovers that she can sense the Wraith. In their search to learn more, Teyla and the Atlantis team discover important information that may hold the key to understanding their enemy, including the disturbing possibility that Teyla's connection to the Wraith could be the result of genetic experimentation.

With the Wraith armada bearing down on the city, the Atlantis team prepares to evacuate. Setting the city's self-destruct sequence, they hope to make it impossible for the Wraith to gain access to Earth. Things begin to look up when reinforcements from Earth are brought in and it is announced that the battleship Daedalus will arrive in four days. However when the warheads are easily destroyed by the Wraith, and the first wave of Wraith attackers strafe the city with weapons fire, it becomes increasingly clear that the added reinforcements are not going to be enough. With time running out, the Atlantis team must turn to the least likely source of aid - the duplicitous Genii! But with the Wraith overrunning the city, even the Genii's help may not be enough.