Rodney McKay makes a momentous decision - to propose to his girlfriend, Katie Brown. Just as he's working up the nerve to pop the question in her plant cultivation lab, however, the room's door slams shut and locks. The city has automatically initiated an emergency quarantine, which means that it has detected a dangerous contagion.
Unfortunately, Katie's lab contains no computer or radio, so McKay can't learn the facts or take action. All he can do is worry. Eventually, he convinces himself that he has caught the fatal disease. As Katie tends to his various "symptoms", he warns her that she will also soon fall sick and die.
All her attempts to cheer him up fail, and then, at this inauspicious moment, she happens to find the engagement ring in his pocket.
McKay and Katie aren't the only ones trapped. Ronon and Dr. Jennifer Keller are stuck together in the infirmary. Keller feels profoundly frustrated to be cut off from sick people who probably need her help, and Ronon, too, is impatient with this forced inaction. The two concoct a bold plan to blast their way out of the infirmary. They don't succeed, but mutual admiration - and attraction - are the unexpected fruits of their teamwork.
Carter and Zelenka, meanwhile, are caught in one of the city's elevator-like transporters. Using Zelenka's tablet computer to get a status report, they discover that Atlantis's communications, scanning, ventilation and even plumbing systems are malfunctioning because of a power spike from an ionospheric storm in the planet's atmosphere. The quarantine is just another malfunction - there is no real contagion.
Locked together in McKay's lab, Sheppard and Teyla access McKay's computer and learn the same information. They also discover a disturbing additional malfunction: The city is broadcasting an automatic distress beacon. Any second now, the beacon could attract a passing enemy ship and lead it straight to Atlantis's top-secret location.
With no time to lose, Sheppard breaks out of a window and climbs up the side of Atlantis's huge central spire, risking his life to reach the control room near the top. Once there, he breaks another window to get in and then shuts down the beacon.
To his dismay, the city's self-destruct mechanism immediately activates. Interpreting Sheppard's broken windows as a sign that the quarantine has been breached, Atlantis is going to respond by blowing itself up. Sheppard must make his way to the city's main power room and turn off the self-destruct, but his mission is doomed unless he can free some of his teammates to help him.