The Administrative Department is headed by the O5 Council. It directs all actions of the Foundation. This department includes all communication nodes and command centers; these centers include reserve personnel for emergencies. Furthermore, the department's authority includes the management of Foundation assets, such as capital usage and budget allocation. Due to the importance of this department, loyalty assessments are conducted more frequently than in other departments. The official archives are under the jurisdiction of this department.

The Intelligence Agency is responsible for searching, tracking, and capturing uncontained SCP entities and gathering information from hostile organizations. Large major facilities always have a disguised intelligence office, most of which are camouflaged as civilian facilities. Intelligence agents are selected from various defense industries, law enforcement agencies, or special task forces around the world.

Foundation operations generally require a large number of elite agents. This is mostly due to anomalies that require significant effort and unconventional approaches for containment. The Mobile Task Force (MTF) was established to handle these matters. MTFs are units of various sizes specialized in performing specific operations in specific situations. All units are named with a combination of a Greek letter and a number. In some cases, they are also referred to by nicknames or callsigns. More detailed information can be found in the Mobile Task Force overview.

Effective scientific research is necessary for the Foundation's existence and activities. The Scientific Department studies contained or newly captured SCP entities and is responsible for designing methods to counter containment breaches, as well as various equipment and pharmaceuticals. Scientific Department staff are scientists handpicked as the best of the best in various fields.

The Foundation's Medical Department is responsible for the health of Foundation employees. Due to the nature of Foundation work, doctors frequently encounter various types of wounds, traumas, infections, or diseases that are difficult to treat and rarely seen in general practice. As a result, the Medical Department is exceptionally staffed with higher-grade personnel compared to other departments. Some Foundation doctors specialize in treating employees suffering from things like mental contamination.

This department is responsible for the safety and protection of all Foundation facilities and subjects. Security Department staff are trained to respond to containment failures, external intrusions, internal riots, natural disasters, or other emergencies. New agents in this department usually receive basic training before being assigned to other sites or entities. Specialized training is conducted after assignment.

A faction that opposes the Foundation. While the Foundation aims to "Secure, Contain, and Protect," the Chaos Insurgency often actively uses anomalous entities to secure military power, technology, information, and political influence. They very frequently attack Foundation sites to invade and plunder them.

Human test subjects used for SCP research. They wear green Foundation jumpsuits.