A method and system for passively regenerating particulate filters, catalyze soot filters and NOx adsorber catalysts for a vehicle having a compression ignition engine having an engine control module (ECM) including an integrated engine and emission system map, and an integrated starter/alternator/flywheel/retarder assembly, comprising sensing the condition of the particulate filters, catalyzed soot filters, and NOx adsorber catalysts and generating an initiate cleaning cycle signal upon sensing that the filters and catalysts require cleaning, monitoring operation of the engine and vehicle to determine the engine speed and vehicle speed and generating an engine speed/vehicle speed operating signal, receiving the initiate passive cleaning engine cycle signal and the engine speed vehicle speed operating signal, and initiating engine control parameter adjustments to modify engine operation to promote passive regeneration of the filters.