High school student Sora Kashiwagi is accustomed to receiving bizarre presents from his father, who is on an expedition around the world. Unfortunately, these gifts have been nothing but nightmares. As a result, when his father sends him a huge package from Egypt, Sora prepares himself for the worst, only to be greeted by Mii-kun—a cute, pint-sized mummy! While initially wary, Sora soon learns that Mii-kun is harmless, a delicate creature yearning for attention. Throughout their amusing day-to-day lives, the unlikely pair meet other people with unique pets, while also strengthening their bond together. Although keeping a pet is a difficult task, Sora is set on caring for the lovable Mii-kun.

After his girlfriend Yuuko breaks up with him, Miyu Samura's luck is at an all-time low. But one day several months later, she reappears and gives Miyu a toy poodle she supposedly cannot take care of. Miyu's knowledge of dogs is nonexistent, and the puppy's rowdiness leaves him in danger of being evicted from his own home. When Miyu decides to take the puppy on a walk, he has a chance encounter with professional dog trainer Shinichirou Niwa and Niwa's well-behaved standard poodle Ourson. In just a matter of minutes, Niwa not only corrects the attitude of Miyu's dog, but also gives Miyu himself stern advice on how to treat his pet properly. Amazed by Niwa's techniques, Miyu decides to quit his job in order to become the trainer's assistant; however, Niwa is not as skillful in dealing with humans as he is with their canine companions. Even so, Miyu refuses to give up on Niwa and his failing business.

Subaru Mikazuki is a 23-year-old mystery novel author, major introvert, and an awkwardly shy person. He would much rather stay home to read a book than go outside and interact with others. Further exacerbating this life of solitude, his parents tragically died in an accident many years ago, leaving him alone in the world. One day, while giving offerings at his parents' grave, Subaru runs into a small grey and white cat named Haru, which he ends up taking home with him. Subaru, however, has never taken care of anyone else in his life—can he even take care of a cat? Haru is grateful toward Subaru, as he gives her all the food she wants—a luxury for a cat who is used to a rough life on the streets. But she notices that Subaru can't even seem to take care of himself! Will she be okay with this dunce? Doukyonin wa Hiza, Tokidoki, Atama no Ue. tells the story of an unlikely friendship between a human and a cat who try to foster an understanding with each other.

A kitten, abandoned and left for dead along with his siblings, is taken in by Tomu Kusanagi, who nurtures him and discovers that the tangerine cat he so adores is actually a genius who can talk, walk, read, and has even acquired a taste for liquor!