A pressure support system (10) includes a pressure generator that generates a pressurized flow of breathable gas to a subject and a processor (22) configured to execute computer program modules. The modules include a first mode module (32) controls the pressure generator according to a first mode of therapy wherein breathing cues are provided to the subject (12) according to a breathing regime. The breathing cues prompt the subject to consciously alter breathing parameters. The modules also include a second mode module (34) controls the pressure generator according to a second mode of therapywherein the flow of breathable gas is provided to the subject (12) at a selected pressure or selectively variable pressures. The modules further include a transition module (36) that transitions between the first mode of therapy and a second mode of therapy wherein parameters of the pressurized flow of breathable gas is adjusted in response to a trigger event.