The player assumes the role of Chris, the protagonist of Popotan. The main characters include three sisters and their maid who live in a western-style mansion. Ai is the eldest of the three and has the ability to communicate with plants. Mai is the middle sister; she is a tomboy and disapproves of Chris's slacker behavior. Mii is the youngest and the most energetic; she often cosplays as "Magical Girl Mii" and helps people out. Their maid Mare appears emotionless at first, but reveals hidden depth later in the story. Popotan takes place in the distant future within the remnants of Tokyo, destroyed by a cataclysm and since altered by geological transformations. The disaster was caused by a giant dandelion structure resembling a spire that arose in the city atop a hill. The main location of the game is a European-style mansion, seen as completely out-of-place in the city. Much of the daytime is spent outside the mansion wandering around town meeting characters and triggering event sequences. Popotan follows Chris's relationship with the girls as well as the mysteries surrounding the spire-like object that caused the destruction of Tokyo in the past. The story opens with Chris, hungry and penniless, arriving in the town where he is to begin working at a convenience store. He wanders around the town looking for a place to stay and comes across a mansion, where he then takes residence along with the sisters and their maid. As the story progresses, Chris begins developing a relationship with the girls. He also meets new friends, including Mai's classmate and Chris's childhood friend Konami, a local shrine maiden named Nono and a mysterious girl named Shizuku.