Sheppard is playing computer golf with Rodney but McKay wants to go meet with Katie and give her an engagement ring. As Rodney heads out, Teyla comes in to talk to Sheppard. Meanwhile, Ronon goes to the infirmary to get patched up by Keller, while Sam and Zelenka share an elevator.
Rodney meets Katie in the botany lab but as he starts to awkwardly try and give her the ring, the entire city goes into shutdown, sealing everyone in where they're at. Communications are cut off as well, and Rodney admits he was tinkering with the quarantine system. Teyla and Sheppard determine it's a Category 5 lockdown and discuss Teyla's removal from field missions due to her pregnancy. She worries about whether she should put herself at risk even after she has her son.
Sam and Zelenka are skeptical whether there even is an emergency, but figure Rodney can take care of it. They're unaware that Rodney is trapped in the botany lab with no access to the systems. Keller tends to Ronon's wound and makes awkward conversation, while Rodney worries that the infection may have already wiped everyone else out. Katie berates him for thinking of the worst-case scenario, noting he must live in a constant state of worry.
Zelenka notes to Sam that Rodney's been a little off his game recently, and they try to access the transporter system through his handheld. Sheppard realizes that Rodney is in the botany lab with no computers or radios and figure he's freaking out. Katie tries to calm Rodney down while Teyla determines there was an atmospheric disturbance that may have caused the lockdown. They'll need Rodney's password, and Sheppard remembers what it is.
As the ventilation starts to make things hot, Sam and Zelenka try to get into the system and he's impressed with both her computer skills and the fact she's removed her jacket. However, they end up short-circuiting the tablet without getting the doors open.
Sheppard determines that the city is broadcasting an emergency signal to warn people away, and it can only be turned off from the control room. Rodney makes small talk about the flower Katie named after him and worries that he has the infection and might have given it to her. Keller worries about the fact she's trapped, unable to help the others, and Ronon tries to reassure her. He notes she reminds him of someone he used to know who put too much pressure on herself, someone who died during the siege.
In the lab, Teyla's baby kicks and she and Sheppard share a moment before she starts to feel ill. He breaks out the window and prepares to climb up four floors to the control room. He manages to get to the control room where Major Lorne is working with the staff to restore ventilation. Sheppard breaks in and shuts down the password with Rodney's password. However, the self-destruct activates and Ronon prepares to break out using a pressurized oxygen tank as an explosive.
It turns out the city armed the self-destruct on its own, set off by Sheppard breaking through the window. They don't know how much time they have so they need to shut it down from the power room six floors down and past several sealed doors, and head out with what C-4 they have.
Katie has Rodney lie down and discovers the engagement ring. Keller prepares to score the oxygen tank to send it flying at the door, but warns the chance of success is minimal. A frustrated Teyla starts climbing the tower but realizes she can't and goes back inside.
Keller has the tank properly cut and Ronon sets it up to drop one tank on top of the other. However, the tank doesn't go as intended and fails to break down the door.
Sheppard, Lorne and the others blast through the door, near where Sam and Zelenka are in the transport. They get Sam and Zelenka out and bring them up to speed.
Rodney doesn't believe that anyone will save them and apologizes for being so fatalistic. Sheppard suggests they go through the ventilation system but only Zelenka will fit so he starts heading for the power room.
Ronon apologizes to Keller, saying at first he thought she was weak. In response she admits there's never been a time in her life where she belonged, and he says she proved herself with the tank, even though it didn't work, then lets her rest her head on his shoulder. They start to kiss just as Zelenka gets to the power room and shuts off the systems then reboots it. The doors open and everyone is freed.
Later, the gang is discussing Zelenka's heroism and Rodney's paranoia. Keller joins them and Sam lets them know that no one seems to have detected their beacon. Rodney goes to see Katie, explain what happened, and admit he has a few minor shortcomings. He says he doesn't think he's ready and Katie admits she isn't either. they make a date for lunch later and say goodbye to each other for now.