Change the parameters used to calculate the fine details of how the internal combustion engine operates, e.g. how much fuel to inject into each cylinder, when to send a spark to trigger ignition, how much pressure should the turbocharger provide, etc.

I can only recommend watching this 2015 talk at German Chaos Communication Congress about the technical details of the scandal. It's in English and really worth watching if you're technically interested. They reverse engineered the ECU configurations and showed how the manipulation works.

https://media.ccc.de/v/32c3-7331-the_exhaust_emissions_scand...