Listen, I have a sister. We're not close —I don't even know how you'd find her. She's the only family I really have, so someone should tell her what happened. And, uh, make it sound good, OK? Tell her I ... I died saving someone ... kids! I died saving kids - a bunch of them.
Scouting through the parts of the city damaged by the recent storm
, McKay and his team of scientists pick up a distress call - two of the team who were checking a different part of the city are being attacked by some unknown menace. They hurry to help, finding one scientist dead and the other sobbing. As the rest of the team look on in horror, the second scientist jumps up, struggles violently against terrifying hallucinations, and then she too drops dead, bleeding from the nose.
McKay surmises that the deaths were caused by some kind of bacterial or viral agent, and asks Dr. Beckett to order an immediate quarantine lockdown on the entire city. Meanwhile, he and his team press forward, on the logic that if it is airborne, they're already infected, and if it isn't, they shouldn't contract it if they're careful. Not everyone is so sanguine, however, and one scientist makes a break for it while the others are examining some ominously broken vials in an Ancient bio-research lab, after he starts having visions and another team member drops dead.
Teyla and Sheppard suit up and go after the escaped scientist, against Weir's direct orders. To make this possible, Weir has to return power to the relevant sections of the city. Sheppard shoots the scientist, but not before he makes it into a teleporter and zaps himself right into the middle of a crowded mess-hall. Some panicking ensues, and then the city itself initiates a much more effective lockdown, even locking Weir and the control room staff out of the main computers.
Meanwhile, Dr. Beckett and his haz-matted medical team have caught up to McKay and the others. The autopsies reveal that each of the victims died of a brain aneurysm at the base of the visual cortex exactly six hours after exposure. The next most recent people exposed, McKay and a team member named Hayes, have already started experiencing the hallucinations. McKay is troubled by the fact that everybody's symptoms have been exactly the same - way too regular for a biological agent - right up until Hayes drops dead and he suddenly becomes much more troubled by the fact that he's about to die.
Except that he doesn't, to everyone's surprise and his own not-inconsiderable relief. It seems that the virus is designed to kill humans
(after terrorizing them with hallucinations) - those with the ATA gene are immune. This isn't much comfort to Ford, who never got the ATA gene therapy, or to Zelenka, for whom the treatment didn't work - and they're next up on the exposure list, about 90 minutes after Hayes and McKay.
McKay manages to find reference to the virus in the Ancient databases, and they learn that it is not in fact biological, but rather caused by nanites. The nanites surprisingly enough do not appear to be self-replicating, so if enough people are exposed they should get too thinned down to be very effective - but nobody really likes the idea of exposing everyone and hoping a few survive. On the other hand, nanites are basically just tiny computers, and should be knocked out by a sufficiently strong EM Pulse
. And as everybody knows, the best way of making an EM Pulse is by detonating a nuclear bomb high up in the atmosphere.
So that's what they do. Sheppard hauls one of the Naquaddah generators to about 20 miles up, sets it to blow, then drops it out of the Puddle Jumper and gets the heck out of there. They know it has worked when the city returns control to the humans and releases the lockdown. McKay speculates that whoever created the virus - assuming it wasn't the Ancients themselves - is someone they definitely
don't want to meet.