The Rehabilitator is a punishment used by Authors on recalcitrant characters to 'rehabilitate' them into better behaviors. The nature of it is never clarified (never described) nor is it ever seen. It is presumably extremely painful/uncomfortable and presumably also works on not-yet-born robotic souls. Whether it works on humans has never been hinted (and therefore unkown). It has been used on Megaman.

The Arrival of Mynd - The Rehabilitator

The Introduction of X - Shadowy Ultimatum