When a marine disappears on a routine patrol of a flooded area of the City of Atlantis, Lieutenant Colonel John Sheppard is determined to find out the truth. But Sheppard has not yet recovered from the effects of his wounding by the wraith tendril in 'The Seed'. Frustrated and in pain, he begins to doubt his ability to carry out his role as military commander. Then, in a terrifying encounter, John learns the true nature of the horror that lurks in the watery depths of his city. Can Sheppard and his team find a way to defeat this malignant alien which threatens not just the members of the Atlantis expedition, but the City itself?