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Rodney McKay decides to propose to his girlfriend, Katie Brown. But just as he works up the nerve to pop the question, a dangerous contagion is detected and the city goes into automatic quarantine. The pair are locked in Katie’s lab, and McKay soon becomes convinced he has the disease.
Ronon and Keller are also trapped by the shutdown and try 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, 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.
Sheppard and Teyla discover that the city is broadcasting a distress signal. Concerned that the beacon could attract a passing enemy ship and lead it straight to Atlantis’s secret location, Sheppard breaks through a window and climbs Atlantis’s central spire to the control room. He manages to shut down the beacon in time, but the city interprets the broken window as a sign that quarantine has been breached and initiates the self-destruct mechanism. Sheppard manages to make his way across Atlantis, freeing the others as he goes, and shuts off the main power. The systems are reset and the quarantine is over. While the others tease Ronon about a possible relationship between him and Keller, McKay realises he is not yet ready for marriage and calls off his proposal.
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