In Josee to Tora to Sakana-tachi, Tsuneo Suzukawa is a university student whose passion for diving and fascination with marine biology keep him focused on one goal: earning enough money through several part-time jobs to study abroad. One night, a sudden accident pushes him off his routine and into the path of a girl in a wheelchair.
The girl is Kumiko, who prefers to be called "Josee." At first she seems rude and impossible to get along with, but Tsuneo is soon persuaded by Josee's grandmother to accept a paid position as Josee's caretaker. He takes the job for practical reasons, hoping to keep saving money for his academic dream, even as he struggles with Josee's bossy behavior. When he finally tries to quit, he learns that Josee has her own wish: to travel beyond the limits of her room and experience the outside world, even while living with her crippling condition.
What begins as an awkward arrangement turns into a shared exploration of the world around them. As Tsuneo accompanies Josee on her adventures, the two discover that the qualities that frustrate them may also be what helps them move toward their respective futures.