His purpose was to provide ways to develop a cure for incurable deadly illnesses, more specifically for Gerald's granddaughter Maria Robotnik, but he was captured and put into stasis by the military when he was deemed as a threat to humanity.
Fifty years later, Shadow was released by Dr. Eggman in order to enlist him in his plan to conquer the world. Initially, Shadow worked with him but secretly sought to destroy the planet in order to avenge Maria.