A method and system removes nuclear, biological and chemical (NBC) agents from an air stream from a facility HVAC. The system includes an irradiation zone, a saturation zone and a precipitation zone. A contaminant detection apparatus controls the irradiation, saturation and precipitation of the air stream. The irradiation destroys biological agents along with saturation of air stream with a water based solution. The biological debris and dissolved chemical agents are precipitated out of the air stream by condenser coils. Nuclear agents are removed from the air stream by diverting the air stream though a bypass filter containing high mass particulate filters and activated charcoal. The contaminants are stored for later removal and destruction. The contaminate detection apparatus includes NBC sensors.