Hot Zone

Hot Zone is the thirteenth episode of the first season of Stargate Atlantis.

Plot
During a post-storm damage survey of Atlantis, Dr. Rodney McKay, Lt. Aiden Ford and a team of scientists and USMC personnel come across one of many Ancient labs. However, upon coming across two of the exploration personnel, the two persons begin seeing hallucinations and suddenly die. Due to the inexplicable nature of the deaths, Dr. Elizabeth Weir asks that all sections of Atlantis be locked down under a self-imposed medical quarantine.

While Dr. Carson Beckett and medical personnel attempt to discern the nature of the contagion, John Sheppard and Teyla Emmagan are training in the art of stick fighting. Sheppard begins to grow impatient, with Weir pointing out that there is nothing for him to do. Meanwhile, Beckett and his team have begun their work on checking out the team members&mdash;and prepping the victims for autopsy.

Sheppard receives word that Peterson, a member of the infected team, has escaped and is fleeing towards Stargate operations and, thus, the hub of the city. Against Weir's orders, Sheppard orders Sergeant Bates to open the doors. Bates does so, offering an after-the-fact apology; "Doesn't really matter now, does it?" replies Weir.

Sheppard manages to catch up with Peterson&mdash;who uses the transporter, ending up at the mess hall. Upon transporting to the mess hall, the city begins to lock down and control to the mainframe is broken. The only two people that can move around safely are Sheppard and Teyla, who procured hazmat suits from a lab. The city's systems appear to recognize that the pair, being so equipped, are definite non-carriers who will be useful in the medical crisis and permit them free access throughout the city.

Meanwhile, results from the autopsies show that the victims died of a brain aneurysm above the visual cortex. As another team member beings to die, McKay theorizes that there must be more to the events. While the visual cortex can be affected, the frightening hallucinations are strikingly similar&mdash;to the point where there had to be another explanation. McKay and Beckett discover that the virus is not organic, but it is a work of nanotechnology. Shortly after this discovery, McKay runs out of time, but does not die. They theorize that the virus does not kill people with the ATA gene, which McKay received in an experiment. While it is designed to kill humans, it appears that the nanovirus is incapable of multiplying, thus limiting their effectiveness.

It was speculated that the nanites could be affected by an electromagnetic pulse. Sheppard goes to an EMP generator in McKay's lab while Teyla goes to the mess hall to comfort the people there. Unfortunately, all doesn't go as planned; the people in the mess area react violently, damaging Teyla's suit in the process. According to McKay, the pulse wasn't strong enough to destroy the nanites. With only 20 minutes until Ford and Dr. Zelenka die, Sheppard devises a plan to detonate a Naqahdah generator above the city. With McKay's help in ironing out the details of the plan, Sheppard flies a Puddle Jumper, releasing the overloaded naqahdah generator 20 miles above the city. (The radiation fallout won't affect the city at this distance, but the EM pulse will be devastating enough to incapacitate the nanites permanently.)

The plan works: the city rescinds the lockdown and the survey team can return to the main area of Atlantis.

While questions loom about who created the virus&mdash;it isn't the Wraith, as they wouldn't create a WMD to kill their foodsource and the Ancients would (theoretically) never reach that extreme; Weir firmly states to Sheppard that the clash in authority is something that should not occur again. Weir also firmly reminds him that Sheppard does not dictate what is and is not a military decision; that's her call. While he reluctantly seems to concede the point, the question is raised as to whether or not this event will occur in the future.