It originally ran consecutively on Sundays from April 6, 2003 to March 28, 2004 with a total of 52 episodes (collectively known as the Japanese "Series 1").
Knuckles and Hawk dig up the red Emerald's hiding place in the subway, but they get into a fight with Eggman's robot, E-91 Lady Ninja, for it.
During the battle, the Emerald is buried under a pile of heavy rock; Knuckles retrieves the "Shovel Claws" to dig it out again.
When a cameraman disturbs an hourglass-shaped stone from a pedestal, ghosts appear and kidnap several people, leaving only Chris and Amy.
The leader of the ghosts, King Boom Boo, mimics Sonic's voice, tricking Amy into placing the hourglass into a slot and strengthening him.
Chris flips the hourglass, freeing the kidnapped people and allowing Sonic and Amy to defeat the ghosts; all the heroes escape, and they seal off the underground chamber.
Sonic reaches the Egg Fort II and recovers the white Chaos Emerald from Lucky.
After Super Sonic destroys the Egg Fort II, Chaos Control occurs and another burst of light appears.
Six months later, Eggman has been quiet, secretly developing an E-100 Series of robots—including E-101 Beta, E-102 Gamma, E-103 Delta, and E-104 Epsilon, each powered by a small animal—on his new ship, the Egg Carrier.
Sonic and co. arrive, and the spirit of Tikal appears, revealing she has kept Chaos dormant with her sadness until Eggman got to him.
Super Sonic fights Perfect Chaos and purifies him, causing him to revert to his base form and allowing him and Tikal to finally pass on.
As they battle the Biolizard in space, Scarlet Garcia broadcasts a message explaining the ARK, and the people cheer for Sonic and Shadow.
The two hedgehogs stop the ARK using Chaos Control, but Shadow doesn't make it back; as the group returns to Earth, Sonic says farewell to him.
Chaos Control at the Space Colony ARK brings in even more of Sonic's world, including the Chaotix Detective Agency, comprising Vector the Crocodile, Espio the Chameleon, and Charmy Bee.
Eggman claims that he will use his giant battleship to stimulate the "belly button of the world", where submarine volcanic chains run through, and destroy the planet.
Shadow, Rouge, and Molly then decide to follow the signature of a Chaos Emerald to the mining site of Cascade.
A total of 13 DVD and VHS volume compilations was released by Victor Entertainment and Universal Music.