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A quarantine lockdown is a means to contain an outbreak of a disease, to prevent it reaching the general population. Atlantis has an automated system that detects and quarantines the infected, but also allows those who are able to help, to enter the quarantine area. This system was first encountered when an Ancient nanovirus was released from the Nanite lab. Unfortunately, the sensors in the area had been damaged by the recent flooding and the system was not activated until Dr. Peterson transported into the Mess hall. (SGA: "Hot Zone")
Four years later, after an ionospheric disturbance, the city entered into a category five lockdown, which sealed every door in the city, disabled all communications and activated a subspace distress beacon. When the city believed that quarantine had been broken, it activated the self-destruct and disabled all computer access as well. (SGA: "Quarantine")