The Turtles sent Raphael - who had been acting unnaturally pleasant - to see the doctor, who soon discerned that he had been affected by a Personality Alterator. He ordered Raphael to bring the Alterator to him, made it portable, and began using it to render cops and guards too "nice" to resist his robberies. Though Raphael was dismayed at this, he couldn't bring himself to stop von Shrink.
The Turtles figured out what was happening and set out to stop von Shrink, but were stopped by his forcefield-encased Phobia Chamber, which brought all their greatest fears to life. Donatello managed to restore Raphael to his usual surly self, and Raphael in turn made von Shrink too nice to resist. He was presumably arrested.