Now that the storm that occurs every 20 years is finally over, the structural integrity of the formally flooded (and previously unexplored) areas of Atlantis needs to be checked thoroughly. Dr. Rodney McKay leads the inspection teams - about a dozen scientists in all. With him are Lt. Aiden Ford and Drs. Zelenka and Hays. Atlantis is judged to be structurally sound. McKay radios Dr. Weir, relays the good news and is about to order everybody home when team members Wagner and Johnson are noticed to be missing. Ford, McKay and Zelenka find them in a dark corridor: Wagner lies face-down, dead. His partner, Johnson, is in a state of panic, screaming about nonhuman entities that are "everywhere." Then she dies, as well.
McKay informs Weir that he has a quarantine situation and needs a containment team, stat. People don't just see things and drop dead; Wagner and Johnson were exposed to something, and it's a good bet that McKay and the others were, too.
Weir is briefed by Dr. Grodin, who advises a citywide self-regulated quarantine. Weir addresses the city: Everyone will stay where they are until the threat is over. Maj. John Sheppard and Teyla have been practicing stick-fighting in the gym; Sheppard's radio has been off. They've only just heard about the emergency through Weir's announcement. Sheppard radios Weir, who tells him to sit tight
McKay backtracks with his people to the place Johnson and Wagner were exploring. It seems to be an Ancient viral lab - and some of the containers are broken. Suddenly, team member Dumais starts screaming about seeing "creatures," grabs her head and dies. Peterson, an engineer, says he has been seeing these creatures for a while now, then he panics. He tries to escape to the upper levels of the city.
Defying Weir's orders, Sheppard and Teyla go to Beckett's medlab, don Haz-Mat suits and go after Peterson. They find him, but he freaks out and runs into a transporter. He ends up in the mess hall, where he dies. The city goes into automatic lockdown - cutting off the control room from the mainframe. Grodin surmises that Atlantis detected the virus and shut itself down. It didn't shut down the lower levels where the virus was released because the flooding must have damaged the detection systems there. Doors open, and the transporters work for Shepard and Teyla because they're in Haz-Mat gear and not detected as a threat.
In the viral lab, Beckett monitors McKay and Hays, who are next in line to perish, according to McKay's calculations of the virus having a six-hour incubation period. Autopsies show that each of the infected died of a ruptured brain aneurysm directly above the visual cortex. The virus seems designed to make people see ghostlike creatures, drive them mad and kill them.
Time's up for Hays. He goes mad and dies. McKay is next. But nothing happens. Why? Because he has the Ancient gene. McKay discovers that they are up against a nanovirus - microscopic machines programmed to kill only humans. Only 48 percent of Atlantis' population can currently accept the Ancient gene, so gene therapy for all isn't an option. McKay tells Sheppard to go to his lab and activate a small electromagnetic pulse generator; the theory is that it'll wipe out the nanites. But the generator is too small. The virus is still alive, indicated by the fact that Atlantis still has itself in lockdown.
A bigger pulse is needed. With McKay and Weir's approval, Sheppard takes a Naquadah generator airborne in a puddle jumper and detonates it 20 miles above the city. Atlantis' systems automatically come back online. The nanovirus is exterminated.
Because the Wraith feed only on live humans, they are ruled out as having created a virus that kills them. That leaves a haunting question: Who invented this horror?