The events of the game take place on the fictional Blood Edward Island. The game's protagonist, Ashley Mizuki Robbins, is the daughter of Richard and Sayoko Robbins, researchers of human memory. After her parents mysteriously went missing in 1994, they were presumed dead.Consequently, Ashley was raised by her father's younger sister, Jessica Robbins, in the suburbs of Seattle. Eleven years later, two days before her fourteenth birthday, Ashley receives a package from her father containing a birthday card and a device called a DAS. The DAS, programmed to respond only to Ashley's biometrics, contains a message from her father, claiming that he is waiting for her on Blood Edward Island.

Assuming control of Ashley Robbins, players navigate through 3D environments and attempt to solve puzzles. During movement, the touchscreen displays an aerial view of Ashley and her surroundings. The player can move Ashley using a point and click system, dragging the stylus across the screen, or using the D-pad. The top screen shows pre-rendered images of the player's current location. To solve puzzles encountered in the game, the player must use the touchscreen, or other DS capabilities, such as the DS microphone.

Two days before her fourteenth birthday, Ashley Mizuki Robbins receives a package from her father, Richard Robbins, whom she thought was dead. The package contained a small handheld device called a Dual Another System, or "DAS" (Dual Trace System, DTS in the American release), along with an invitation to meet him on Blood Edward Island. The following day, her and her aunt , Jessica Robbins, set off for the island. While there, Ashley meets "D", a ghost with no memories, who has been wandering the island alone for decades since his death. Ashley attempts to aide D in uncovering his lost memories, while also uncovering the truth about her father, the murder of her murder, and the mysterious project, code named "Another".