Hydrogen as a vehicle fuel can be used in two different ways. As you say John, a petrol fuelled engine can be converted to run on Hydrogen, however the low energy density means a very inefficient use of the fuel and you still get NOx emissions from the exhaust as well as water vapour.
The second way is to use a hydrogen fuel cell to generate electricity to drive an electric motor used to power the car. Hydrogen fuel cells are much more efficient than internal combustion engines and produce a very much cleaner exhaust.