When an approaching storm with awesome destructive capabilities causes Dr. Weir to evacuate the city, the Genii launch an invasion, and take control of Atlantis' weapons. With Dr. Weir and Dr. McKay taken hostage and Major Sheppard fending for himself against the ruthless Genii troops, the rest of the Atlantis team desperately tries to find a way to get back to the city while the storm rages around them.

While assessing the structural damage to the city caused by a massive storm, two of Dr. McKay's team of scientists experience horrifying visions. Minutes later, they drop dead. Retracing the steps of the dead scientists, McKay and his team find an Ancient lab, its contents in disarray. Afraid of a viral outbreak, Dr. Weir places the city under a self-regulated quarantine. Even with the city under lockdown under the threat of a possible viral outbreak, more and more people begin suffering from the same terrifying visions. If McKay cannot find a cure, the entire city will be doomed.