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After an overnight rain, the Passat will not start. Where is water likely getting into the motor and what part is it affecting?

A lot depends on the age (model year and odometer mileage) of the car.
Whether the car is up to date with maintenance is also relevant.
Unfortunately, you failed to provide all of that very important information.

In the absence of that info, I would advise the following:

If the car is under warranty, this problem is the dealership’s problem to diagnose and to resolve, not yours. Take it to the dealer–multiple times if necessary–with this complaint until it is resolved. If no improvement takes place, telephone VW at the corporate level. Contact info is in your Owner’s Manual.

If the car is not under warranty, I would suggest that you replace the spark plug wires. Wires that are more than 4 or 5 years old can develop microscopic cracks that admit moisture and interfere with the flow of current to the plugs. If the car has a distributor (newer ones don’t), then you may also have to replace the distributor cap.

Depending upon the exact model year/odometer mileage/engine type/state of maintenance of this car, there may be other approaches that will be necessary, but in the almost total absence of vital information, I have given you the best actions at this point.

How old are the spark plugs and the plug wires?  

Next night you expect rain, spray the spark plug wires with WD-40.  That is one of the few things WD-40 is really good at.

If it works with the spray, then plan on new wires. 

You also may want to go out early in the morning (before the sun starts up) and open the hood and watch the plug wires while someone tries to start it. If you see sparks you are looking at the problem.