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Sonic the Hedgehog has been taken by security personnel and is being held hostage inside of a plane, unfortunately for them, Sonic is able to break free and escape with his snowboard. He lands on a street inside a bustling city, cars zooming in from all directions. After the initial snowboard sequence, he proceeds on foot, destroying any robotic henchmen, and escaping from the city. Eventually, a chase scene occurs between Sonic and a G.U.N truck, in which Sonic successfully escapes. He meets Shadow the Hedgehog. He fights off a giant robot, codename: BIG FOOT and meets Shadow the Hedgehog for the first time, showing off the power of a chaos emerald. Shadow departs, and leaves Sonic in the middle of a street, and is surrounded by a huge army of military personnel.
- Note: The opening cutscene plays in both Hero Mode and Dark Mode
In another part of the world, Knuckles and Rouge the Bat are fighting over the Master Emerald, when Dr. Eggman arrives to steal it. Knuckles attempts to stop Eggman, but ultimately shatters the Master Emerald into several smaller pieces. Knuckles and Rouge race to see who can collect the emeralds first. Knuckles explores the windy canyon and manages to find all three pieces of the Master Emerald.
Tails is seen flying over a military base, questioning whether or not Sonic has been behind the recent events. Tails spots Dr. Eggman chasing after Amy Rose and decides to land on the island and save her. After beating Eggman, Amy and Tails proceed to head inside the prison and rescue Sonic. Amy agrees to release Sonic and give him information regarding Shadow if he'll marry her. Sonic disagrees and is released and rushes off, leaving Amy behind.
Sonic appears outside on the actual base of the airport and attempts to get off the island by taking a giant rocket that is about to launch, and he manages to makes it to the other side of the island, which is a vast jungle. He meets up with Shadow and the two exchange words and fight. Sonic and Shadow reach a standstill and Dr. Eggman alerts Shadow telling him to get off the island before it explodes, and he glides off, leaving Sonic to go through the jungle.
Sonic must escape the forest within the time limit. After Sonic makes it to the end of the level, a cutscene showing the island and nearby harbor exploding, Tails and Sonic just barely making it out.
Knuckles is shown exploring a mountainous region, noting how spooky the place looks, but remembers his mission at hand. After finding the three chaos emeralds, he manages to find a path to an underground mine.