TECHNOLOGY FOCUS - ELECTRICAL POWER AND ENERGY - Preferred System: In the system above, the controller includes a stack hydration model that estimates the amount of water in the fuel cell stack at system shut-down to determine the length of the first stage purge. A length of the first stage purge is determined based on how long it will take the hydration level of the stack to asymptotically reach the known hydration value. The known hydration value is about 48 g of water in the stack. The desired hydration level is about 23 g of water in the stack. Desired hydration level is three water molecules per each sulfonic acid molecule in membranes of fuel cells in the fuel cell stack. The first stage purge includes using humidified cathode air that has a relative humidity level less than 100%. The cathode air is used to purge either the cathode side or the anode side of the fuel cell stack or both. Purging the fuel cell stack during the first stage causes the hydration level of the fuel cell stack to drop to the known hydration value in an asymptotic manner. The known hydration value is about 48 g of water in the stack for a stack having approximately 300 cells and 400 cm2 of active area per cell. The desired hydration is about 23 g of water in the stack for a stack having approximately 300 cells and 400 cm2 of active area per cell. Desired hydration level is approximately three water molecules per each sulfonic acid molecule in membranes of fuel cells in the fuel cell stack. The first stage purge includes using humidified cathode air that has less than 100% relative humidity. The cathode air is used to purge both the cathode side and the anode side of the fuel cell stack. Preferred Method: Purging the fuel cell stack with humidified air includes purging the fuel cell stack with humidified air so that the hydration level of the fuel cell stack asymptotically drops to the known hydration level. Purging the fuel cell stack with dry air includes purging the fuel cell stack with dry air until the fuel cell stack reaches a desired hydration level of about 23 g of water for a stack having approximately 300 cells and 400 cm2 of active area per cell. The method further comprises using a stack hydration model for estimating the stack hydration level before purging the fuel cell stack with humidified air to determine how long to purge the fuel cell stack with humidified air.