The Security Department (SD) is SCI-Pathos' main armed combative department, responsible for protecting the Foundation's assets and ensuring the safety of its civil personnel. While in-game, Security personnel are tasked with guarding various key locations in Site Phi while also maintaining control over the facility's Class-D population in Site Omicron. As the facility's main security force, they are also responsible for ensuring that civil departments can carry out their duties unimpeded by misbehaving Class-Ds, rogue personnel and hostile forces. This includes, but is not limited to: Escorting events hosted by civil personnel, responding to Class-D riots and escapees, fighting off hostile forces during raids conducted by Groups of Interest, and securing anomalous items studied by the Scientific Department. Members of the Security Department can expect to work alongside members of the Mobile Task Forces —Pathos' smaller and more specialized combative force— in order to reach these ends.

The bulk of the department consists of unspecialized Security personnel referred to as "Base SD". These members are the backbone of the Security Department's presence in-game, and are typically tasked with the department's less difficult and lower-risk duties. The department also contains subdivisions that are equipped to handle the duties which require advanced training, knowledge, and/or equipment that Base SD members do not have access to.

These subdivisions include the Combat Support Unit (CSU), the Military Police (MP), and the Security Response Unit (SRU).

Each of the subdivisions have their own requirements and entry process which are tailored to the duties their members will be expected to fulfill in-game. Security personnel can also gain access to more duties and equipment by ranking up in the main group, with each rank playing its own role in the department's in-game hierarchy and opening up new duties for members to carry out.

The Security Response Unit (SRU) is responsible for responding to riots and engaging hostile personnel within the Foundation's facilities. The Security Response Unit specializes in quick mobilization and special tactics & drills to ensure that the aforementioned tasks are succeeded.

The Military Police is a unit within the Security Department responsible for maintaining order and public peace within the installation. They play a vital role in ensuring the smooth operation of the site and can assist with investigations, providing escorts, patrolling highways, guarding anomalies, and responding to emergencies. This unit places a strong emphasis on public safety, peace, and order, and works closely with the Ethics Committee.

The Combat Support Unit (CSU) is responsible for and in charge of all support-based operations around the installation. Primarily assisting Security Personnel and Mobile Task Forces in their duties with the addition of biohazard safety and containment, the Combat Support Unit specializes in quick healing tactics, tactical suppression, defensive combat, battlefield logistics, and emergency response.