There is a rumor in Kamome Academy that somewhere within the school premises lies a clock that governs the passage of time in the academy. That clock is overseen by three clock keepers—each representing the past, present, and future. Despite this, an unforeseen event causes mayhem, with students rapidly aging and the academy's infrastructure falling apart.

Nene Yashiro and Kou Minamoto seek help from Hanako-kun, embarking on a new adventure to find those responsible for this mess. However, what they uncover is more than just the culprits' identity. As hidden truths are revealed and new vows are established, the academy students and its apparitions find themselves in a game of fate, where the living fight to free themselves from its grasp.

Jibaku Shounen Hanako-kun 2 was released on Blu-ray and DVD in a box set on June 25, 2025.