Hot Zone

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

Synopsis
While exploring sections of the city that were flooded during the storm, some of the scientists start dying after seeing realistic hallucinations that cause brain aneurysm. Their attempts to contain it don't go well, as one of the infected goes into a populated section of the city.

Plot
During a post-storm damage survey of Atlantis, Dr. Rodney McKay, Lt. Aiden Ford and a team of scientists and United States Marine Corps 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, Major John Sheppard and Teyla Emmagan are training in the art of Bantos 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 and prepping the victims for autopsy.

Sheppard receives word that Dr. 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 Sgt. 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, who uses the Atlantis 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 begins 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 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 Nanites. Shortly after this discovery, McKay runs out of time, but does not die. They theorize that the virus does not kill people with the Ancient Technology Activation 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 Electromagnetic pulse 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. Radek Zelenka die, Sheppard devises a plan to detonate a Naquadah generator above the city. With McKay's help in ironing out the details of the plan, Sheppard flies a Puddle Jumper, releasing the overloaded Naquadah 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, it isn't the Wraith, as they wouldn't create a WMD to kill their food source 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.

Notable Quotes
Zelenka: 7,549.

McKay: Oh, please. Prime. 4,021.

Zelenka: Ah-ha, nice try. Not prime. Okay. Lt. Ford, uh, 599.

Ford: I don't care if it's a prime number or not.

Zelenka: Oh come on. Yes or no?

Ford: No.

Zelenka: (laughs) It's incredible. 10 for 10.

McKay: He is terrible.

Ford: So I suck at prime/not prime. Somehow I'm going to sleep tonight.

Zelenka: At this point, it's gone way beyond not knowing your prime numbers.

McKay: It's a true/false game. Statistically, just by guessing, you should be getting at least half of these right. Look, 993.

Ford: Prime.

McKay: Oh, come on. That's an easy one. Are you hearing this, Hays?

Hays: Not really. I guess I've been too busy doing my job.

(After Ford has managed to fail all his prime number guesses)

Zelenka: Lt. Ford, would you mind being the subject of research papers on statistical improbabilities?

Ford: Is this some sort of payback for guys like me beating up guys like you in high school?

(during combat training)

Teyla: You have not been practicing.

Sheppard: Yes I have.

Teyla: If this was really a fight -

Sheppard: If this was really a fight, I would have shot you by now.

Beckett: Just try to stay calm.

Ford: Calm?! You told me I have a million tiny robots running through my veins whose only purpose is to terrorize and kill me. You stay calm!

McKay: Look, you seriously have to stop interrupting my last thoughts. I mean, this is important stuff you need to hear. Now- if you're here for more than a year, I've left some notes on how to roll blackouts to effectively maintain your power requirements and-and, oh, tell everyone that I was, I was inches away from a Theory of Unification but uh, uh, the notes, they were lost when I died saving the ...

Zelenka: ... kids.

McKay: Yeah. (Pause) Ok. I should be dead now.

(Major Sheppard is on his way in a Puddle Jumper to drop a naquadah generator converted into a bomb)

McKay: You'll only have 30 seconds to release it before it explodes, you need to get as far away as you can.

Sheppard: "Get as far away from the nuclear explosion as possible." That's good advice, Rodney. Thanks.

Goofs

 * When planning to detonate an Electromagnetic pulse, which would deactivate all vulnerable technology within the city, they make a show of turning off all computers and similar equipment brought with them from Earth. However, their radios remain in operation during the EMP and are not interfered with in the least, when in actuality they would have been rendered non-functional. (This may be because the first EMP didn't reach the Control Tower .)
 * In the beginning of the episode, during Dr. Radek Zelenka's and Dr. Rodney McKay's game of "Prime or Not Prime", Zelenka erroneously answers that 4021 is not prime, even though it is.
 * The hazmat suits Teyla Emmagan and Major John Sheppard wear aren't air tight as seen by the detached helmet.
 * McKay erroneously refers to nanotechnology as machines on the scale of billionths of a millimeter, instead of the proper scale of billionths of a meter (or millionths of a millimeter).

Character

 * Dr. Biro