Eight months after defeating Doctor Robotnik,[c] Sonic the Hedgehog attempts to help the public as a vigilante to little success. Tom Wachowski, Sonic's caretaker, advises Sonic to remain patient for the day his powers will be needed before he and his wife Maddie depart for her sister Rachel's wedding in Hawaii. Sonic plans to have fun while home alone but is attacked by Robotnik, who has returned with the help of Knuckles the Echidna. Knuckles desires to honor the legacy of his extinct tribe and demands the location of the legendary Master Emerald, an ancient relic that allows its possessor to bend reality to their will.
Sonic is rescued by Miles "Tails" Prower, a two-tailed fox who idolizes him and comes to warn him about Knuckles. Sonic convinces Tails to help him find the Master Emerald, while Robotnik reunites with his assistant Stone and, scheming to steal the emerald, offers to help Knuckles. Sonic and Tails follow clues on a map from Sonic's dead guardian Longclaw to Siberia, where they find a compass within an old temple. Robotnik and Knuckles track them and pursue Sonic and Tails down a mountain. During an ensuing avalanche, Robotnik and Knuckles steal the compass. Tom rescues Sonic and Tails by using a ring to teleport them to the wedding.
Rachel's fiancé Randall and his wedding guests reveal themselves as undercover agents of the Guardian Units of Nations (G.U.N.) and capture Sonic, Tails, and Tom, who are then saved by Maddie and a vengeful Rachel. Robotnik and Knuckles find a large water temple containing the Master Emerald. Sonic goes to the temple and fights Knuckles while Robotnik uses the distraction to seize and fuse himself with the emerald, which explodes and sinks the temple into the water. Sonic and Knuckles escape and agree to work together as Tails rescues them in a biplane.
In Green Hills, Robotnik uses his new abilities to create a giant robot resembling himself. Sonic, Tails, and Knuckles work together to fight the robot and its accompanying drones and to reclaim the Master Emerald, but it breaks, splitting into the seven Chaos Emeralds. Tom and Maddie rescue Sonic, who uses the Chaos Emeralds to transform into Super Sonic. He destroys the robot before dispersing the Emeralds and reverting to normal. Knuckles fixes the Master Emerald from the remaining shards and agrees to guard it with Sonic and Tails. The three resume an idyllic life with the Wachowskis.
Stone infiltrates G.U.N. as it begins searching for Robotnik in the mech's rubble. An agent reports to G.U.N. Commander Walters that a 50-year-old file hidden in G.U.N’s database containing coordinates to an off-site research facility, which houses Shadow the Hedgehog, has been uncovered.
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