Sonic and his friends are off to visit the mysterious Flicky Island. According to legend, the island contains precious gems - among them the Chaos Emeralds. Sonic must find the Flickies, mysterious little birds who hold the key to finding the gems. Flickies are rarely seen, and it is said that thier existance is tied closely to the location of the Chaos Emeralds.

Meanwhile, Dr. Robotnik has hatched a new scheme. His target this time is Flicky Island. He has detected the presence of the Chaos Emeralds on the island. Upon arriving there, Robotnik immediatly starts setting up intruder defences, and begins building the robots he loves so much. But Robotnik needs to find the Flickies to place inside his machines. Suddenly, in the distance he sees a bright shining Dimension Ring appear. A flock of Flickies fly out of the ring, perch on a tree branch, pick up some food, and then disappear into the Dimension Ring. "So they live in another dimension, do they? Hah! I've found the secret to the Flickies!"

The Flickies travel freely between dimensions using the Dimension Rings! Without wasting anytime, Robotnik develops a new device: the Dimension Ring Generator. He captures Flickies from the Flicky dimension using his new device, and begins turning them into robots. Later on, Sonic and his friends arrive at Flicky Island, and find the place in pandemonium.

Sonic sees the doctor busily placing the Flickies into his robotic shells. "Robotnik!" Sonic yells.

"Sonic? Again? Well, no matter. With the robots I've created using the Flickies, you'll never be able to stop me! At last I'll be free to find all the Chaos Emeralds and rule the world!" Sonic realizes he must save the Flickies by freeing them from thier robotic prisons and sending them back into the Flicky dimension. More importantly, Robotnik must not be allowed to find the Chaos Emeralds first. Time to go, Sonic!