An integrated duct system is utilized to admit an antimicrobial vapor into a vehicle to decontaminate the contents and surfaces of the vehicle and subsequently to remove the vapor. The ducts comprise an air conditioning and/or heating duct, a decontamination duct for admitting an antimicrobial vapor, an auxiliary circulation duct for diffusing the vapor throughout the vehicle, and an aeration duct for removing the vapor from the vehicle, as well as a catalytic converter for detoxifying the antimicrobial vapor before removal. The integrated decontamination system is suitable for the chemical or biological decontamination of vehicles, provides enhanced vapor delivery and distribution on a rapid basis and also provides for rapid aeration for removing the antimicrobial vapor.