Sonic has been missing for two months when Dr. Eggman discovers something impossible on an abandoned racecourse: one section of a concrete loop looks completely solid, but rocks thrown at it pass straight through. Curious and intrigued, Eggman brings Shadow, Amy, Tails, Knuckles, and Rouge to investigate. They enter the strange opening and find themselves trapped in the actual Backrooms, beginning in the endless yellow halls of Level 0. The entrance disappears behind them, leaving them with no obvious way home. As they explore, they encounter increasingly strange environments, impossible architecture, distorted physics, strange sounds, and entities that resemble twisted versions of themselves. Some are enormous and unnaturally tall, while others are smaller and much faster; all have disturbing numbers of eyes scattered across their bodies. The creatures sometimes chase them, sometimes imitate their movements, and sometimes simply stand in distant hallways watching. They also hear footsteps, breathing, scratching, voices calling their names, and noises coming from places that should be empty. Despite all of this, they never encounter a Sonic mutant or creature resembling Sonic.

The group must travel through numerous Backrooms levels, each with its own environment, dangers, and rules. They encounter yellow office-like corridors, industrial areas, electrical stations, abandoned offices, hotels, dark underground spaces, flooded areas, caves, parking structures, schools, malls, hospitals, forests, and countless other impossible locations. Tails attempts to map their surroundings, but the Backrooms constantly change, while Eggman tries to understand the phenomenon scientifically, Knuckles relies on his strength, Amy keeps everyone emotionally together, Rouge notices subtle changes and suspicious details, and Shadow becomes the group’s main protector and scout. Shadow is especially affected by the Backrooms because its constantly shifting environments undermine his sense of control; he becomes increasingly vigilant, memorizing sounds, checking corners, watching reflections, and refusing to let anyone wander alone. Throughout their journey, they repeatedly find signs that Sonic may have passed through the Backrooms—scratches, markings, scattered belongings, and messages—but never actually find him. The deeper they travel, the more it seems the Backrooms knows who they are and is deliberately testing them, separating them, imitating them, and using familiar voices to lure them away. Their ultimate goal becomes finding out what happened to Sonic, discovering whether an exit truly exists, and surviving long enough to escape the endless levels together.