The agency, is actually called the Office of Emergency Management (OEM), and is responsible for oversight and development of New York City's emergency management plans. OEM also operates the City's Emergency Operations Center (EOC) where city, state and federal agencies join representatives from the private and non-profit sectors to coordinate complex responses to disasters and other emergent situations.
In "The Strain" Season 3. The building seems to be mostly active because of the outbreak. Justine Feraldo also plans to extend the secure zone to various parts of the five boroughs such as Brooklyn, Queens, Manhattan, Staten Island, and Bronx. The office is open 24 hours a day, seven days a week, dedicated to help secure New York.
Vasiliy Fet comes back to the office to debrief her on the status of the Navy Seals sweep of vampire nests in Chinatown. Justine Feraldo emphasized to Vasiliy Fet about the need of more soldiers to secure a greater part of Manhattan.
Thomas Eichhorst plans to create a bioweapon bomb to infect everybody in the office by strapping C-4 explosive inside the vampire's torso, who have not turned completely. Once the nondescript vampires got into position, the explosives were detonated, the white and worms were dispersed in all directions infecting everyone in sight, including Justine Feraldo, a worm manage to get into her eye but was cauterized by the UVC light. Eph conducted a preliminary exam on Justine Feraldo for the strigoi infection. He said that the test will have to be repeated in two hours, to confirm the diagnosis. Once the alloted time passed, Eph repeats the diagnostic protocol, and she is found free of contagion, Justine Feraldo was pleased as Ephraim Goodweather left the room.