F.E.A.R. 2: RebornEdit
The Replica Command seems to be compromised of a group of clones that are specifically trained in coordinating offensive/defensive measures. After Alma Wade's release, she inadvertently reactivates the Replica Forces, resulting in all of the forces' allegiance blindly shifting to her side.
While it is Alma who reactivates the forces, the command seems to direct the forces' every strategic movements. It is implied that the command was created to guide the clone soldiers in case psychic commanders were inept with tactics.
The command has only been mentioned during F.E.A.R. 2: Reborn, where it actively takes part in coordinating Foxtrot 813's mission until he goes rogue. The command is represented by an image of a Replica Heavy Soldier in 813's HUD (Heads Up Display). Throughout the course of Reborn, the command is forced to deal with the rogue 813, the remnants of Armacham Technology Corporation Forces, and overall paranormal menace surrounding the city of Fairport.
There is an easter egg where the command is briefly heard: 
While the command is not mentioned directly, the fact that Replicas are seen working alongside Armacham Technology Corporation Forces imply that the Replica Forces' chain of command is broken and absorbed into the corporation's mercenary ranks to contain the situation of the Almaverse.
- It is unknown if there are several commanding authorities for each variant of the Replica Forces, as only the seventh variant's leadership is confirmed so far.
- Replica Command is the start-up announcer for Replica side in multiplayer mode, like Colonel Vanek, he updates the status for Replica team.