In a post-apocalyptic world where an environmental disaster led to the eruption of Mt. Fuji and the inundation of Yokohama, the age of humans is in its twilight. Alpha Hatsuseno is an android and the namesake of a small cafe outside Yokohama. As her owner is away on a trip indefinitely, she has been left responsible for running the cafe. Although she rarely gets any customers, Alpha remains outgoing and cheerful.

While Alpha awaits her owner's homecoming, she explores the vicinity with her scooter and camera. Throughout her journeys, she meets new people and other androids, making memories along the way.

Yokohama Kaidashi Kikou is a beautiful, laid-back story centered around Alpha's daily activities, emphasizing the passing of time in everyday life.