On the lush, tropical paradise of South Island, Sonic the Hedgehog's animal friends begin disappearing one by one. When he discovers that the evil scientist, Dr. Ivo Robotnik, has been kidnapping them and converting them into robotic Badniks as part of a plot to collect all six of the fabled Chaos Emeralds, Sonic decides it's up to him to save them, and embarks on a quest to free his friends and thwart the evil schemes of Robotnik.
Sonic Origins shows how Sonic discovered Dr. Robotnik’s plan; while on a quick run, he discovered that a Moto Bug was attacking some Flickies. With no time to waste, Sonic immediately defeated the Moto Bug and freed the Flicky trapped inside the robot. After recovering from its dizziness, the Flicky Sonic freed points him in the direction of some Buzz Bombers carrying capsules filled with trapped animals, led by Dr. Robotnik. Determined to stop the evil scientist, Sonic goes after Dr. Robotnik, leading into Green Hill Zone.
As Sonic races through the Zones of the island, he engages in numerous confrontations with the nefarious Robotnik and his deadly machines, and one by one frees the animals from their robotic shells and capsules placed at the end of almost every zone. In their final confrontation, the Doctor prepares his last dastardly contraption to end his adversary, but proves no match for Sonic's awesome might, and his machine is totaled. Fleeing with his tail between his legs, Robotnik abandons his laboratory as it explodes, crumbling to scrap, with Sonic narrowly escaping. Following his escape, Sonic finally returns to the vast Green Hills where his journey began.
In the game's normal ending, Sonic gives the player an annoyed look before posing for the screen, and Robotnik will be shown after the credits juggling any undiscovered Chaos Emeralds the player missed, with a "Try Again" message taunting them.
However, if the player succeeds in collecting the six Emeralds by the end of the game, the player is rewarded with the good ending, where the six Chaos Emeralds react to one another and release a burst of light before disappearing, rejuvenating the wildlife and nature of South Island, leaving Sonic astonished before he jumps up towards the screen and poses. In the post credits scene, Dr. Robotnik is shown humorously stomping on the "End" text in a tantrum fueled attempt to crush it, to no avail.
