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 a 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.