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The runaway (pun intended) success of the first Sonic the Hedgehog film and the sequel hook all but guaranteed that the Blue Blur would return to the silver screen, though there be hiccups along the way. Sonic 2 would proceed without Ted Elliot and Terry Rossoin who were both already too committed to Rampage to participate in the production and Dreamworks thus brought on screenwriter (and Solid Snake voice actor) David Hayter on board. However, executives were not completely satisfied with the script and hired Buffy the Vampire Slayer creator Joss Whedon to polish it, which added some needed wit as well as make Amy Rose less a damsel in distress and a more proactive player in the story.

Sonic the Hedgehog 2 is--for all intents--an adaptation and expansion of the third video game (Sonic 3 & Knuckles) where throwaway details such as the mural from Hidden Palace Zone play a central role in the story. The film begins with the Death Egg crashing into Angel Island with Dr. Robotnik exploring the surrounding area and stumbling upon both the mural and the Master Emerald when the island's guardian, Knuckles, confronts himself. Dr. Robotnik deceives Knuckles into believing that he's a kindly scientist and informs the doctor of the prophecy behind the mural. His long-lost civilization predicted the coming of a great evil that would claim the Master Emerald and doom their home. Robotnik notices a physical similarity between the "hero" of the mural, and twists the truth so that he convinces the naive Knuckles into believing Sonic is the great evil that's coming to steal the Master Emerald.

What follows is a noticeably faithful adaptation where Knuckles steals the Chaos Emeralds from Sonic and his friends at Robotnik's request and runs interference while the Doctor repairs the Death Egg. This culminates in the fated showdown between Sonic and Knuckles before Robotnik reveals his true intentions and steals the Master Emerald, forcing the Blue Blue and Rad Red to combine forces to save Angel Island and destroy the Death Egg. An upgraded and almost T-1000 like Metal Sonic makes his return for a battle royale with Knuckles, Tails, and Amy in the Sky Sanctuary while Sonic pursues Robotnik for a confrontation in outer space.

The increased production budget gave the second film a noticeably higher quality of animation that many critics noted rivaled and even exceeded Disney's Mulan in some parts, particularly the "Doomsday" sequence where Super Sonic chases a fleeing Robotic through a meteor swarm. However, Sonic the Hedgehog 2 made slightly less than its predecessor, but was highly profitable nonetheless. One observation made by fans and critics was the absence of the Buzzbomber and Motobug, which was well-received as they were a point of contention with latter and the slightly more serious tone brought in from their absence demonstrated a film that was growing up with its audience.

Many fans wondered what Sega and Dreamworks had in store and would be pleased when they saw the mid-credits scene where a deactivated Metal Sonic lay buried under the rubble of Sky Sanctuary when his eyes flcker back on--setting up the plot for the final film in the trilogy.