- All right. Look, I know you're probably panicking right now, but there is no time for that. You need to focus. I'm sure you're wondering who tied you to the desk. Look, the truth is, it was you ... I mean, me. I did it 'cause I needed you to get this message. It would take too long to give you the full explanation and you wouldn't remember it anyway, so you're just gonna have to trust me on this. It is vitally important that you find this woman. Don't worry about anything else and for God's sake don't trust anyone. Just find her and do it fast, because if you don't, hundreds of people are gonna die including you.— McKay's recorded message to himself
The episode opens on McKay alone and tied to his desk in a darkened city. Fortunately, there's a message waiting for him...from him. He's suffering from amnesia - and so is everyone else, apparently. The recorded message tells him to find Teyla at all costs (and includes a handy picture), so he cuts himself free and heads out.
14 hours earlier, McKay is visiting Dr. Katie Brown, whose botany team has just returned from the mainland. She has named a new species of cactus after him - Rodneyana valosa. When she complains of headaches and dizziness, they head down to the infirmary, where Dr. Keller reveals that she's the eighth person to come in for the same complaint in the last hour. It is caused by a bacteria, presumably picked up on the mainland, and the entire city has been exposed. What's worse, it is soon revealed that as it progresses the disease causes amnesia...and then death.
Carter suspends all gate travel, and just to be sure, makes Zelenka remove the gate's control crystal. As more and more people start forgetting who they are and what they're doing, Sheppard dispatches Major Lorne round them up and hold them in the mess hall for their own protection.
Back in the present, McKay wanders the corriders looking for Teyla, and finding no one. Suddenly, he comes across Zelenka, armed with a metal pipe, and warning about soldiers shooting everybody and taking them away. He himself has been constantly on the run evading capture. Major Lorne and his troops arrive and Zelenka runs off, but McKay is captured and taken to the mess hall. Teyla isn't there, and he manages to mobilize the rest of the patients to stage an escape. McKay and Carter make it out and reconnect with Zelenka. The three of them track Lorne, who leads them straight to Teyla in Atlantis's holding cell.
It turns out Teyla and Ronon are immune to the disease, which is a mutated version of a common Pegasus galaxy childhood ailment. Ronon and Sheppard are off on the mainland collecting the plant which cures it, and McKay had been working on configuring a fast distribution method when Teyla was captured and his memory finally gave out. They let Teyla out of the cell and she directs McKay back to the override he was working on so that he can finish it. Ronon and a completely amnesiac Sheppard arrive back with the plant via jumper - whereupon they are promptly captured by Lorne's squad. Ronon directs Lorne to his own pocket - which contains a photograph of Sheppard and a note saying "This is your commanding officer. Trust him." Lorne yeilds the floor to Sheppard, who yeilds the floor to Ronon. The plant gets distributed via the ventilation system and everyone begins the slow path to recovery.
- Amnesia Danger: Everyone in Atlantis. Lorne and his team are able to retain more of their memory as they have been taking stimulants, but unfortunately, they've forgotten that they've been taking them for too long, making them highly erratic. Furthermore, while they remember that their last order was to round up everyone into the Mess Hall, they've forgotten this doesn't include the people working to cure the disease.
- Anachronic Order / How We Got Here
- Crouching Moron, Hidden Badass: Zelenka, evading Lorne's team on his own and even knocking one of them out.
- "Die Hard" on an X: Not the main plot, but at least parts of the episode are "Die Hard starring Zelenka!"Lorne: He [Zelenka] gave us the slip. Must have heard us coming. Cracked one of my people over the head with a metal rod and disappeared down a service hatch before I could get a shot off. There's no telling where he is now.
- Hoist by His Own Petard: It was pre-amnesia McKay's idea to have the soldiers relocate everyone to the mess hall.
- Human Notepad: Rodney writes instructions for himself on his arms and hands with a marker.
- The Immune: Ronon and Teyla, due to having antibodies from contracting the common (non-lethal) strain as children.
- Laser-Guided Amnesia
- Note to Self:
- Rodney leaves one when he realises he's starting to lose track of what he was doing.
- Lorne also has one, although it's just a picture of Sheppard with a label explaining who he is and that he can be trusted.
- Shout-Out: Rodney starts writing notes and directions on himself with a marker, not unlike the protagonist of Memento.
- Stock Episode Titles: 8 uses.