The Wraith assault on Atlantis rages on. In the midst of the chaos, Dr. Beckett treats Lt. Ford, who has been rescued from a near-fatal encounter with the alien invaders. Ford's abnormally quick recovery, however, leaves the doctor suspicious. He worries that the Wraith who attacked Ford might have injected the young officer with a harmful enzyme, causing unpredictable long-term damage.
Meanwhile, far above the planet and surrounded by Wraith, Maj. Sheppard faces seemingly certain death - until he is rescued by Earth's newest and most sophisticated space battle cruiser, the Daedalus. Commanded by Col. Steven Caldwell, the Daedalus has completed its long journey to the Pegasus galaxy just in time. With its help, the Atlantis team defeats the Wraith's first assault on the city.
Their victory, however, is short-lived. The next wave of the Wraith onslaught - an entire fleet - is bearing down on Atlantis. With a little over a day before the new attack, Dr. Weir realizes that even the Daedalus will be no match for the Wraith's redoubled forces. The team's only hope is a drastic plan devised by Dr. McKay - but the complicated technology it requires might take too long to perfect.