It's a brushless cooling fan with built-in electronics. I am using the transistor as a relay to shut the fan off when cooling is not required. So it's not PWM or anything. I do not have access to the windings, just the power supply lines as a whole. I am not commutating the fan at all, it's being done internally. I am just switching the power on and off. I am wondering if there is already a free wheeling path inside the commutation electronics.
I am not chopping the voltage with PWM or anything, it's just a remote on/off switch for the fan.