Knuckles is struggling to adjust to home life in Green Hills due to his warrior lifestyle which even affected Maddie Wachowski's plans to have her house rebuilt after Dr. Ivo Robotnik's attack. Taking Sonic's advice to make himself at home too far, a furious Maddie grounds Knuckles. After soliciting advice from his deceased Echidna elder Pachacamac, Knuckles takes up Wade Whipple, who was recently kicked from his bowling team for the upcoming tournament at Reno, Nevada, as his apprentice; Wade decides to let Knuckles accompany him to Reno for the tournament. As they begin their trip, they are tracked by corrupt G.U.N. agents Mason and Willoughby. They intend to capture and sell Knuckles to the mysterious Buyer who supplies them with weapons configured from Ivo's technology and powered by Knuckles' quills. At a roadside bowling alley, Wade confides to Knuckles that he was deserted by his father at a young age, leaving him with abandonment issues. Using a ring portal, Mason and Willoughby appear to battle Knuckles; he defeats Mason, but Willoughby takes advantage of the distraction to trap Knuckles in a cage, and they escape.

Mason and Willoughby take Knuckles to a ski lodge to await rendezvous with the Buyer. Armed with a pair of Mason's weaponized gauntlets, Wade comes up with a plan to sneak in and rescue Knuckles. Though his plan fails, with his squad car being destroyed in the process, Wade outsmarts the agents and saves Knuckles. They find a truck to use to escape, with Wade teaching Knuckles that not every victory needs to be righteous. At daybreak, they learn from the radio that Wade has been branded a fugitive, so Knuckles suggests finding a hiding place, and Wade reluctantly decides on his childhood home.

Wade and Knuckles lay low at Wade's childhood home in Boise, Idaho, where they are greeted by Wade's Jewish mother, Wendy Whipple, and his older sister Wanda, an FBI agent. Wendy is overjoyed to see her kids home, having prepared for the family's traditional Shabbat dinner, but Wade is despondent, due to constant mistreatment from Wanda throughout his childhood. That night, tensions quickly boil between the Whipples, and Knuckles learns about the family customs from Wendy. Wade secludes himself in his room, where Knuckles learns that Wade's reason for wanting to go to the tournament is because his father, bowling champion "Pistol" Pete Whipple, will be competing. A group of bounty hunters learn of Wade's wanted status and strike at the house, but Knuckles and the Whipples manage to dispatch them, allowing the family to reconcile as they watch the Shabbat candles dim.

The next morning following the Shabbat dinner, Jack Sinclair, a bounty hunter and Wade's former best bowling partner, kidnaps Wade to turn him in for the reward money. Knuckles chooses not to rescue Wade, deciding to use the experience to teach Wade independence. Unable to escape, Wade is advised by Knuckles to visit the "Great Battleground in the Sky" for guidance. Wade successfully visits the afterlife, which takes the form of a bowling alley, where Pachacamac teaches him through a low-budget rock opera of Knuckles' origins. Wade comes to learn that a warrior's greatest strength is their heart, allowing him to escape and challenge Jack to a joust, which he wins. With newfound confidence in himself, Wade and Knuckles continue on to Reno, now joined by Wendy and Wanda.

Knuckles and the Whipples arrive in Reno where Wade confronts and reconciles with Pete. With his relationship with his father seemingly resolved, Wade moves up the ranks in the bowling tournament, pitting him against Pete in the finals. Meanwhile, Mason and Willoughby are forcefully taken to the Buyer who reveals that he is a former agent of Ivo and Willoughby convinces him to give them one last chance to recapture Knuckles. Witnessing him and Pete bond, Wendy warns Wade that Pete will eventually leave him again. Visiting Pete's rooftop penthouse, Wade finds Mason and Willoughby holding Wendy and Wanda hostage, revealing Pete sold them out to keep Wade out of the tournament. With his family's lives at stake, Wade is forced to lure Knuckles into the penthouse where Mason and Willoughby prepare to ambush him.

Having been secretly tipped off by Wade, Knuckles avoids the trap and fights the agents, while Wade frees his family. Knuckles defeats the agents by re-directing a pair of ring portals that suck them up, trapping them between dimensions when the portals collapse on themselves. Wade proceeds to the tournament to challenge his father in the finals, while the Buyer confronts Knuckles outside using a giant mech suit. Wade rolls a perfect game to defeat Pete, but during Wade's celebration they are interrupted by Knuckles and the Buyer's fight. The Buyer catches Knuckles and drains him of his power, but Wade stands up to him, holding off the Buyer with the help of his mother and sister. Knuckles eventually regains consciousness and reabsorbs his power, activating the Flames of Disaster technique as he and Wade manage to defeat the Buyer. Pete attempts to flee with the trophy, but he is subdued by Wendy and Wanda, as Wade and Knuckles celebrate before heading back to Green Hills.