On the distant planet Mobius, Sonic, an anthropomorphic blue hedgehog who can run at supersonic speed, is unexpectedly followed by a tribe of echidnas. His guardian, an anthropomorphic female owl named Longclaw, gives him a bag of warp rings that open portals to other planets. She uses one to send him to Earth while she stays behind to hold off the echidnas, leaving Sonic alone.

Ten years later, Sonic enjoys a secret life near the town of Green Hills, Montana, but longs to make friends. He idolizes the local sheriff Tom Wachowski and his veterinarian wife Maddie unaware the pair are to relocate to San Francisco as Tom plans to accept a post with the SFPD.

One night, Sonic grows upset over his loneliness while playing baseball alone and inadvertently triggers an electromagnetic pulse that causes a massive power outage across the Pacific Northwest while running at high speeds. The United States Department of Defense reluctantly enlists the services of eccentric roboticist and scientific genius Dr. Robotnik to determine the cause. Seeing he is being hunted, Sonic plots to leave Earth for a different planet; he is reluctant to do so as the planet only consists of fungi. However, Tom discovers Sonic in his shed and shoots him with a tranquilizer dart, causing Sonic to accidentally create a portal to the Transamerica Pyramid's tower roof upon reading the writing on Tom's shirt. Sonic accidentally drops his bag of rings on the tower's roof before he passes out. Tom hesitantly agrees to help Sonic and the two flee when confronted by Robotnik, who falsely labels Tom a domestic terrorist. The two slowly bond, with Tom relating to Sonic's desire for friends. Sonic creates a bucket list and Tom helps him complete several entries along their journey.

Meanwhile, Robotnik, discovering that one of Sonic's quills holds an almost limitless amount of electrical energy, plans to capture Sonic to use his powers for his machines. As he tracks them down, Sonic and Tom manage to fight off several mechanized drones sent by Robotnik, but Sonic is injured in the battle.

Arriving in San Francisco, Tom brings Sonic to Maddie, who treats him at her sister Rachel's home. Sonic receives a new pair of red sneakers to replace his ruined ones from Rachel's daughter Jojo. The group heads to the roof of the tower and recovers the rings as Robotnik arrives in an advanced attack hovercraft and his flight suit powered by the quill. Sonic fights off Robotnik's drones and uses one of his rings to send Tom and Maddie back to Green Hills to protect them; however, Robotnik uses the quill's power to match Sonic's speed. Sonic fights Robotnik in a chase across the world before Robotnik subdues Sonic in Green Hills. Tom and the townsfolk intervene, and Tom acknowledges Sonic as his friend, causing Sonic to regain his power. Sonic takes back his quill's power from Robotnik, weakening Robotnik's hovercraft. Sonic also promises himself that he would use his power to protect his friends. Using his powerful spin attack, Sonic viciously attacks Robotnik and defeats him by banishing him into a portal to the mushroom planet.