Dr. Robotnik has taken over Mt. Mobius and turned it into a mechanical base. He is using energy from the magma flowing under the volcano to power his Veg-O-Fortress. He also has the power to transform helpless animals into robots. Sonic the Hedgehog must take down this fortress to free the enslaved animals.
The only way to make that happen is to trigger an eruption in the volcano it's build on. Sonic knows this can be done by removing the Chaos Emeralds that keep the volcano stable. However, Dr. Robotnik is also aware of the fragile relationship that exists between the Emeralds and the mountain, and he's set up an elaborate pinball defence system to make sure the precious jewels don't go anywhere.