Like Yume Nikki, .flow mainly takes place within Sabitsuki's dream world, located in her PC. However, this game has a much darker tone within its dream world, often featuring body horror and motifs touching upon a possibility of hospitalization. The dream world is filled with often large, looping areas, occasionally housing an Effect. Due to its bizzare and surreal presentation, active interpretation of various areas, characters, and events are required in order to fully understand the nature of .flow.
.flow centers around a girl named Sabitsuki, who is confined in her apartment with only a balcony to view the outside world. Inside her apartment, the only three activities she can do is to play Famicom game Shinsoku Neko, sleep in her bed (which allows her to save), and play .flow on her computer. When she decides to play .flow, she is immersed into a surreal dream world existing within her PC, and thus is where most of the content of the game is accessed.
While in .flow, the main goal is to collect all twenty-four effects, which are scattered throughout the dream world. These effects are gained usually through interaction with one of Sabitsuki's various dream characters, and give her new abilities once these effects are used. In doing so, Sabitsuki must avoid the ever-present Kaibutsu, who can send her to an inescapable world that can be escaped only through awakening. Once Sabitsuki drops all of the effects on her computer in the dream world, she enters what is referred to as the "endgame."
Once the endgame is reached, the player assumes control over Rust, a person similar in appearance to Sabitsuki. Unlike Sabitsuki, Rust cannot use any effects, and all of the Kaibutsu transform into Red Demons instead, who deal physical damage to Rust instead of transporting her to an inescapable area. This makes Rust more vulnerable to the dream world; however, one advantage is that she has access to any areas that Sabitsuki were unable to enter. In these new accessible areas, Rust must find three empty boxes that allow her to access the final area and complete the game.
Unlike Yume Nikki's single ending, .flow has three different endings available throughout the game. These endings depend on whether or not the player has accessed the endgame, and if they have found all three empty boxes.