In each mission, the agency infiltrates a facility belonging to one of the corporations. The facility is the “level” or “map” where the mission takes place. Except for the Tutorial mission, facilities in Invisible, Inc. are procedurally generated, meaning the layout of each facility is random, and you will not see the same facility twice.

Facilities are made up of rooms, connected by doors, and there are some common features which are present in all or most facilities. Each facility is protected by guards and other security measures, depending on the corporation and the mission difficulty. However, the layout of the facility itself is not affected by these factors.

For many of the rooms in a facility, the shape and size of the room, and the positioning of mainframe devices, cover objects and other decor are random. Other rooms are prefab rooms, pre-designed and included into the facility layout. Each facility has approximately 10 rooms, plus a starting room, any objective rooms, and an exit room. Some rooms may be “joined together”, resulting in non-rectangular shapes; this means the number of “rooms” can be less than 10.

Some routes between rooms may be blocked by locked doors, or an Emitter which is either impassable or passable with a penalty. Except for some objective rooms, and the exit room at mission difficulty 6 and higher in Endless mode, there is guaranteed to be an alternative route which does not require you to unlock any doors or disable the Laser Panel. However, this route may sometimes be much longer.

The starting room is the room which your agents teleport into at the start of the mission. The starting room is always a prefab room; in typical facilities, each corporation has a few possible prefab starting rooms, while special missions have their own prefab starting rooms.

The starting room can contain a Console, but never mainframe devices such as Security Cameras, nor guards. Additionally, in Beginner mode, guards never patrol into the starting room from another room.

The exit room contains the transport pads which your agents must use to teleport out of the mission. The exit room is a prefab room. In typical facilities, the prefab exit room is a 6×3 corridor with 2×2 transport pads at the side, and distinct decor. Unlike other prefab rooms, this exit room can contain Security Cameras, and can occasionally be “joined together” with another room, so in practice it is not always a 6×3 corridor.

Like all rooms except for the starting room, the exit room must be discovered by exploring. In typical missions, exiting the facility is the only compulsory objective, so finding the exit room is an important goal. At mission difficulty 6 and higher in Endless mode, the exit room is only accessible through an exit door, which must be unlocked using an Exit Access Card.

There is no exit room in the OMNI Mainframe mission, and other special missions have their own prefab exit rooms which cannot be “joined together” with other rooms. In the OMNI Foundry Lab mission, the starting room is also the exit room.

A guard entrance is a walled-off 2×2 area where guards enter the facility. Each guard who spawns during a mission will spawn inside a random guard entrance, either at some alarm level, because of Validate or a mission-specific event, or when an Enforcer respawns. Additionally, civilians who are panicking will exit the facility by running to the nearest guard entrance and teleporting out.

All facilities have two guard entrances, except for the OMNI Foundry Lab mission which has three. The doors to a guard entrance cannot be opened or peeked through by the player.