All Rumi Yokoi wants to do is focus during school, but she is constantly distracted by Toshinari Seki, her neighboring classmate. Paying attention during class is the least of Seki's worries, as he obsesses over intricate setups created using an assortment of items, from an elaborate domino course on his desk to a treacherous war played out with shogi pieces. Yokoi desperately attempts to focus in class, only to be repeatedly sucked into his intriguing eccentricities; however, they always seem to end up with her getting in trouble with their teacher. Fortunately, lessons will never be dull with Seki's antics around!

Kaori Sasaki—a member of Uchihama Academy's Astronomy Club—confesses to Sou Akiyama, but later that evening, she dies in a tragic road accident. Her friends and fellow club members mourn her death in a local hospital. Yet she shows up to school the following day, and no one senses anything amiss. The day finishes without any unusual incidents, and the group of friends plans for the upcoming cultural festival. Suddenly, the room is shaken by an unnatural earthquake. Everyone splits up to investigate—except for Nagisa Hanamiya, who stays behind. As everyone leaves, Nagisa notices that the odd relic-like cube that she was toying with starts emitting a strange blue light. Meanwhile, Sou stumbles upon an unconscious, naked girl lying in a pool of water. Ushinawareta Mirai wo Motomete follows the Astronomy Club's increasingly bizarre adventures—from dealing with ghosts to quelling unrests between student clubs. All the while, they unravel the circumstances behind the sudden appearance of a new transfer student.

Several generations after the original Yatterman series, Leopard lives with her mother and guardians, Dorothy, Voltkatze, and Elephantus, just outside the prosperous Yatter Kingdom. She lives a happy if impoverished life, unaware of her ancestral ties to the infamous Doronbow Gang, until she discovers a mural of Doronjo, Boyacky, and Tonzura in a sealed off area of her home. It turns out that Dorothy, Voltkatze, and Elephantus are descendants of the villainous gangsters, which is why they have been forbidden from entering the hero Yatterman's Kingdom! At first, Leopard vows to never engage in villainous actions like her ancestors, but new circumstances may mean that she must go back on her word, donning the identity of villain in search of true justice.