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While engaging in a fight with his nemesis, Dr. Eggman, Sonic the Hedgehog destroys the Paradox Prism, an ancient artifact with immense power. This causes a ripple in the space-time continuum, separating Sonic from his friends and sending him to New Yoke City, a dystopian version of Green Hills in a parallel universe ruled by five Eggman variants. Traveling through his new surroundings, Sonic is confronted by Nine, a variant of his best friend Tails who constructed mechanized tails as weapons against his childhood bullies, not having a Sonic to help him. Sonic earns Nine's trust, and the young genius modifies Sonic's shoes and gloves to attune to the new energy in his body from the Prism. However, Sonic and Nine are captured, and Sonic is taken for tests run by Rusty Rose, a variant of Amy Rose turned into a subservient cyborg. When the variants threaten Nine, Sonic overworks his powers, causing him to generate a massive amount of energy. However, he notices what seems to be a hallucination of his rival Shadow the Hedgehog during this surge and flashbacks to an earlier confrontation with him.

A power outage gives two rebels a chance to break into a lab where the Chaos Council is studying Sonic's strange connection to their energy source.

To secure the Prism Shard, the rebels battle the Chaos Council. Then Sonic makes a startling discovery about the events that shattered his world.

In a dimension called the Boscage Maze, Sonic runs into tree-dwelling versions of his friends who warn him of a monster that lives on the jungle floor.

To find his way back to the right dimension, Sonic have to fight with the jungle monster who waged war on his friends and capture the powerful Prism Shard.

Sonic returns to New Yoke City, where the resistance has rallied the citizens into joining the uprising. However, Nine is a no-show, and Sonic has to deal with the fallout of his sudden disappearance.

A surprise portal brings Sonic to a world covered in ocean water where his friends are a band of pirates and needs their help to find another shard.

As Sonic and his crew set sail for the next shard, they encounter Rusty Rose. After a long battle Sonic ends up getting in contact with the shard only to be confronted by Shadow in the Shadowverse. Shadow sends and enraged kick as Sonic