One Christmas Eve, Hana, Gin, and Miyuki are rummaging for presents through heaps of garbage when they chance upon an abandoned baby in the cold winter night. Appalled at the pitiful sight, Hana's maternal instincts kick in and she insists on finding the baby's biological mother to demand an explanation. Naming the baby Kiyoko—meaning pure child—they begin their search using the possible clues left alongside her: a mysterious key and a single note. However, their plans are soon thrown into disarray as they get caught up in a series of unprecedented events. Tokyo Godfathers follows the journey of the trio as they stick together through thick and thin, hoping to deliver Kiyoko to her true home, and find their very own Christmas miracle.

It is said that a picture is worth a thousand words. In this case, it holds an infinite amount of secrets. These are secrets that only Cheng Xiaoshi and Lu Guang are able to find. In a small shop called Time Photo Studio, the two friends provide a special service: using their extraordinary powers that let them enter photographs, they jump into pictures brought to them by clients in order to grant their wishes. Through the eyes of the photographer, they live through the events surrounding the picture and try to decipher how to solve their client's request. But every time they jump into a picture, they take a great risk. One wrong move and they could alter the future of the person who took the picture... and possibly countless other events too. So when the events they are forced to live through in these pictures start to become personal, it will take the utmost strength to push their feelings aside and focus on accomplishing the task they were paid to do.

Beginning his first year of high school, all Matsuboshi Raidou wants is to make friends—starting with the cute, tiny, and soft-spoken Reina Aharen, who sits right next to him in class. Unbeknownst to Raidou, Reina shares the same sentiment, but she has a problem. Awkward and timid, Reina is incapable of determining how chummy she has to be when approaching a person. Due to Reina's complete inability to gauge personal space, the two struggle to spark their unlikely friendship, as even the simplest tasks like talking seem impossible for them. But despite the countless yet pointless challenges that hinder the pair, the overly imaginative Raidou will do whatever it takes to befriend the indecipherable Reina.

When her newly-built home is razed to the ground by an earthquake, low-achieving, clumsy, and troublesome third-year high school student Kotoko Aihara is forced to share a roof with the school's—and possibly Japan's—smartest student, Naoki Irie. Kotoko is not actually a complete stranger to Irie-kun; unfortunately, a single love letter that she tried to give him in the past has already sealed her fate as far as he is concerned. Throw in some quirky friends and a meddlesome mother, and Kotoko might not even have a snowball's chance in hell of winning the older Irie boy's heart. Yet Kotoko remains optimistic that, because she now lives in his house, her unattainable crush on the genius since the beginning of high school has never been more within reach.