The Mutual Defense Force's main headquarters is the Tower 61 facility on Terra Secundus. Construction began on this facility in 2201 and lasted four years. It is a huge monolithic structure that is built deep into the planet's crust and stands almost 1,500 meters tall. Its base at ground level is 300 meters in diameter which contours into a needle shape as one travels to the 30 meter diameter top.

The roots of Tower 61 are almost 300 meters below the crust. These levels house power plants, support systems, archives, and various research facilities. This building is self-contained and can produce its own gravity, oxygen, water, and food. These systems are located in the sublevels also.

The 440 surface levels house administration, operational , educational and other offices. The High Command also maintains the command, communication, and control facilities needed to coordinate the fleets throughout the Core. Housing, recreational, and restaurant facilities are also present.

The tower is protected by an unspecified number of defensive systems that include a molecular harmonizer and two interceptor squadrons. In addition, a cadre of Omega Guards are always on duty here patrolling the interior and exterior of the facility.

Forty thousand personnel are assigned to this facility. Almost thirty percent of them are berthed here also. Others commute from other locations around the planet. A typical tour of duty here lasts three or six years.

The operations of command and control are conducted through a sophisticated communications network called ICCPN (Interstellar Command Control Protocol Network). It is a multi-layed system that includes satellites, communication probes, and secured Nexus uplinks. Every corner of MDF patrolled space can be observed from this building. Every military installation can be monitored from this facility. Every form of conveyance can be tracked by these systems. In a sense, there is very little that happens throughout the Federation that is not recorded.

Ships on patrol are always in constant communication with the ICCPN. The data collected by ship sensors are relayed back instantaneously, to provide the command and intelligence staff with constantly updated information. In turn, the High Marshal and his two ranking advising admirals can use the ICCPN to take control of a starship in deep space. To date, this is an option that has never been used. In theory, it would only be used in catastrophic events such as mutiny or the death of the crew.

Although Tower 61 is the MDF's primary location, it is rumored that two other redundant facilities have been built in top secret locations in the event of an emergency.