Haruto Kirishima lived a calm life out in the countryside, away from the fast-paced life of the city. Then Yuzuki Eba appeared in his life out of nowhere, having come from Tokyo to briefly live with her family. Their time together left him enamored with the memories of that short period before she just as abruptly disappeared from his life, and left him full of questions. Kimi no Iru Machi begins some time later, after Haruto moves to Tokyo to live with his sister, in order to pursue a career as a cook. In reality though he wishes to be with Yuzuki. Things don't start good though. When he arrives he is mistaken for a burglar and attacked by his sister's neighbour Mishima Asuka. After the misunderstanding is cleared his feelings begin to waver though. Is Eba, who keeps avoiding him for seemingly no reason, the one for him or is it Asuka?

Yurume, an 18-year-old "ronin" and recent high school graduate, has high hopes of being accepted and attending Tokyo University. She moves into an apartment complex, the Maison du Wish, located on the outskirts of Tokyo where other ronins living there are studying for upcoming college acceptance exams.

For the average Japanese high school student, walking to school can be a chore, but for first-year Chio Miyamo, it's always an adventure. Constantly running late due to her long night sessions playing video games, she is forced to come up with new routes to make it to Samejima Private Academy on time. On her many bizarre journeys to school, Chio contends with obstacles like street-blocking detours, overzealous kabaddi players, and befuddled motorcycle gang leaders. But these minor hindrances are no match for the special ops training that Chio, AKA the legendary assassin "Bloody Butterfly," has received from her extensive gaming obsession. Together with her best friends Manana Nonomura and Yuki Hosokawa, Chio will do whatever it takes to avoid her school's harsh penalties for tardiness. [Written by MAL Rewrite]

The continuation of Yurumates 3D right after the first season.