Siren is divided into several scenarios, each taking place in one of Hanuda's ten sublocations, and organized chronologically in a table called the Link Navigator. In order to complete a scenario, the player must accomplish a primary mission objective that usually involves reaching an exit point, subduing certain shibito, or finding an item. Objectives in different scenarios are interconnected via a butterfly effect, and a character's actions in one scenario can trigger a secondary objective in another. Examples of such actions include obtaining keys, unlocking doors, or otherwise interacting with items unrelated to the current mission objective. Scenarios can be replayed any number of times once completed.
The game's defining feature is the characters' collective ability to "sightjack," or see and hear from the perspectives of nearby shibito, humans, and other creatures. The process is similar to tuning into a radio frequency, with serving as the dial. The clarity and location on the dial of each target depend on the distance from and orientation to the player, respectively. Once a signal is found, it can be assigned to one of the controller's four face buttons to easily switch between multiple signals. Via sightjacking, the player can discover a shibito's position, patrol route, locations and items of interest. However, the player is unable to move during this time and thus vulnerable.
Eschewal of direct engagement with shibito is heavily emphasized in order to progress through the game. Characters can walk silently, avoid the use of flashlights during dark scenarios, and crouch behind objects to elude detection. Certain mission objectives require the use of items and the environment to create distractions that will displace shibito from their usual positions. Others require the player to escort and issue commands to a non-playable character. The player can also shout at any time in order to call the attention of nearby shibito.
When a shibito hears a suspicious sound, it will search in the general direction of the sound's origin. If a character enters the shibito's line of sight, it will actively pursue the character and attempt to kill him either with a weapon or by strangulation. The shibito will also shout to alert others nearby shortly after it spots the character. Once the character has remained out of sight for a period of time, the shibito will give up and resume its usual habits.
Depending on the scenario, the player either begins with a weapon, obtains one during the course of the scenario, or lacks it throughout. In melee combat, the player can use either a regular quick attack or a slower, more powerful attack. While shibito can be defeated in combat, they cannot be killed and will reanimate after a period of time, briefly remaining in a suspicious state. Similarly, if a character is injured, he can recover after a period of time. Characters will lose stamina during combat and while running.
The in-game map displays the surrounding area and the player's directional orientation, though it does not indicate the player's current location (only the start and end points). Instead, the player has to distinguish where he is by noting and orienting himself via certain landmarks on the map.
There are also miscellaneous items scattered throughout each scenario that give the player further insight into the story's background. Once obtained, these items are placed into a catalog called Archives and can be viewed at any time during the game.