The titular scenario centers around Sora's rescue effort of Kairi. Assuming an incorporeal form, Sora travels back in time to the battle between the guardians of light and the Organization, traveling through the guardians' hearts to reach Kairi.

After passing through the hearts of Ventus, Aqua, Terra, and Roxas, Sora enters his past self's heart and tries to avert Kairi's fate, but fails. However, Mickey reveals to Sora that Xehanort has hidden the crystal fragments of Kairi's heart as a last resort.

Sora finds five fragments in Scala ad Caelum before his past self's final battle with Xehanort, and then traces the remaining two through Riku and Mickey's hearts during the guardians' battle against Xehanort's replicas, restoring Kairi.

After defeating Xehanort's merged replicas, Sora and Kairi travel to the Final World to meet Chirithy, whom Sora persuades to return to the realm of light. Sora and Kairi then visit their friends' worlds—reuniting Chirithy with its owner, Ventus, and restoring Naminé's heart—before returning to the Destiny Islands, where Sora vanishes.

The "Limitcut Episode" is set one year after Sora's disappearance; his allies have since lead an ongoing search for him, while Kairi has entered stasis after volunteering as Ansem the Wise's test subject to help Sora. During a visit to Radiant Garden, Riku analyzes digital copies of Sora and the Organization's members programmed into Cid Highwind's computer, hoping to uncover clues to Sora's whereabouts through their battles.