On a cold, snowy night in New York City, an ordinary citizen named Lucas Kane finds himself under the control of an unknown force and murders a stranger in a diner. Once he comes to senses, Lucas realizes he must escape while leaving as little evidence as possible behind. Barely managing to accomplish that, Lucas contacts his brother and tries to understand what has caused him to commit the crime, recalling the events of his own past in the process. Meanwhile, two police detectives investigating the murder, Carla Valenti and Tyler Miles, are determined to find the perpetrator, at the same time trying to deal with the personal problems of their lives.
Indigo Prophecy is a psychological thriller where the player controls different characters on both sides of a murder - the killer and those who are trying to find him. The game's core gameplay style is adventure, with three protagonists exploring various locations, talking to other characters, and interacting with the environment to advance. However, the game features action-oriented sequences, including tasks that must be completed within a limited amount of time and quick time events, which require the player to press the correct button during a scene.
The game emphasizes realism in the player's interaction with the environment. For example, picking up a rag and cleaning the floor requires the player to move the mouse or analog stick back and forth, imitating actual movements of the object. Dialogue with characters often imposes time limits on the player; failure to choose an optimal response in time will prompt the game to choose another, not always the optimal one. The player's choice will sometimes influence subsequent events and the outcome of the entire story, eventually leading it to one of three possible endings.
The game's cinematic treatment is evident in its handling of action-based gameplay and cutscenes, which are often seamlessly integrated into each other. An example of this is the split-screen technique used during dramatic moments: while the player completes required actions on one screen, another displays what is happening around the controlled character.