When microbial contamination is introduced into a room (20*) of an enclosure, such as a building, an HVAC system including supply ductwork (16) and a return ductwork (34) is decontaminated with hydrogen peroxide vapor. A decontamination controller (46) operates controllable baffles (22) at outlet registers (20), temporary controllable baffles (44) at inlet registers (30), and a blower system (10) to circulate hydrogen peroxide vapor from hydrogen peroxide vapor generators (42) through the ductwo...