- 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.— Rodney McKay, last words.
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.
- Deus ex Nukina
- EMP: Used to destroy the nanites.
- Foreshadowing: It is implied at the end of the episode that the nanites were invented by a faction other than the Ancients or the Wraith. In Season 3, it is implied that the nanites were most likely the work of the Asurans.
- Final Speech: McKay finally gets to complete one (see page quote) after having tried unsuccessfully before.McKay: Look, you seriously have to stop interrupting my last thoughts. I mean, this is important stuff you need to hear.
- Hazmat Suit: Sheppard and Teyla put such suits for the emergency and find that Atlantis' systems somehow sense that they are properly equipped for the emergency during its lockdown and opens doors for them.
- I Resemble That Remark!: Sheppard's insistence on breaking out of the imposed quarantine to stop the infected Dr. Petersen, risking getting infected himself and spreading the virus to the rest of the city, actually makes him just as much of a danger as the man he's determined to stop. Weir even points this fact out. This rather foolish and rash decision does at least get somewhat mitigated shortly afterwards, due to Sheppard and Teyla finding and donning a pair of Hazmat suits. Not only does this allow them to safely go after Petersen, it turns out that Atlantis' sensors can tell they are in no danger of being infected and permit them to move through the quarantine zones freely.
- Mistaken for Dying: McKay, as usual. To be fair, nobody expected him to be immune.
- Neglectful Precursors: Verging on abusive for whoever created the virus, since it's never made clear whether the Ancients created or merely discovered it. Season 3 however heavily implies that it was the Ancients and a forerunner of their research into creating the Asuran Replicators.
- The Plague
- Zombie Infectee: Albeit with Nanomachines instead of Zombies. Dr. Petersen continues to insist he's not infected even when displaying obvious signs of illness.